Locus 5503

Sequence ID 3L_DroMel_CAF1
Location 15,089,699 – 15,089,849
Length 150
Max. P 0.996769
window8701 window8702 window8703

overview

Window 1

Location 15,089,699 – 15,089,815
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.77
Mean single sequence MFE -20.79
Consensus MFE -14.63
Energy contribution -16.48
Covariance contribution 1.85
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.70
SVM decision value 1.53
SVM RNA-class probability 0.961683
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15089699 116 - 23771897
UAUAAGCCC-ACAAAAA-AG-UGUAUAAAAAGCCUA-AAAGGCACCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUUGAUAAGGGUUUCACUUGCAAUUAUGAGCCCAUUAAUUUUC
.....((.(-((.....-.)-))........(((..-...)))..................)).....(((((((((((((.((((.......))))))))))))).))))......... ( -26.00)
>DroSec_CAF1 6982 118 - 1
UAAAAGCCCCACAAAAA-AG-UUUAUAAAAAGCCUACAAAGGCACCGAACAAAUGUAAACUGCAAUUUUGGGUCAUAAUUGAUAAGGGUUUCACUUGCAAUUAUGAGCCCAUUAAUUUUC
.................-((-((((((....((((....))))..........)))))))).......(((((((((((((.((((.......))))))))))))).))))......... ( -25.94)
>DroSim_CAF1 7581 118 - 1
UAUAAGCCCCCACAAAA-AG-UUUAUAAAAAGCCUACAAAGGCUCCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUUGAUAAGGGUUUCACUUGCAAUUAUGAGCCCAUUAAUUUUC
(((((((..........-.)-))))))...(((((....))))).........(((.....)))....(((((((((((((.((((.......))))))))))))).))))......... ( -26.70)
>DroEre_CAF1 6997 101 - 1
UAUAAAACC-ACAAUAA-ACCU-UAAUAAAAGCCUAAAAGGGCACUGAAUAAAUUUACAAUACAAUUUUGGGUCAUAAUUGAUA----------------ACAUGAGCUCAUUAGUUUUC
...(((((.-.......-....-........((((....)))).........................((((((((........----------------..)))).))))...))))). ( -10.50)
>DroYak_CAF1 7025 104 - 1
UAUAAAACC-ACAAAAAAACCUUUAUCAAAAGCCUAAAAAGGCAACCAACAAAUGUAUAAUACAACUUUGGGUCAUAAUUGAUAA---------------AUAUGAGCUCAUUAAUUUCC
.........-...........((((((((..((((....))))..((((....((((...))))...)))).......)))))))---------------)................... ( -14.80)
>consensus
UAUAAGCCC_ACAAAAA_AG_UUUAUAAAAAGCCUAAAAAGGCACCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUUGAUAAGGGUUUCACUUGCAAUUAUGAGCCCAUUAAUUUUC
...............................((((....)))).........................(((((((((((((...(((......))).))))))))).))))......... (-14.63 = -16.48 +   1.85)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,089,739 – 15,089,849
Length 110
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 82.79
Mean single sequence MFE -24.91
Consensus MFE -18.17
Energy contribution -19.68
Covariance contribution 1.50
Combinations/Pair 1.17
Mean z-score -2.02
Structure conservation index 0.73
SVM decision value 0.92
SVM RNA-class probability 0.882718
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15089739 110 + 23771897
AAUUAUGACCCAAAAUUGCAGUAUACAUUUGUUCGGUGCCUUU-UAGGCUUUUUAUACA-CUUUUUUGU-GGGCUUAUAUUGCCCUGCUUUUUCGG--UUUCUAUUGUUGGGUCC
......(((((((....((((.......))))..((.(((...-.((((.......(((-......)))-((((.......)))).))))....))--).)).....))))))). ( -25.40)
>DroSec_CAF1 7022 112 + 1
AAUUAUGACCCAAAAUUGCAGUUUACAUUUGUUCGGUGCCUUUGUAGGCUUUUUAUAAA-CUUUUUUGUGGGGCUUUUAUUGCACUGCUUUUUCGG--UUUCUAUUGUUGGGUCC
......((((((.....(((((..((.......((((((...((.((((((..((((((-....)))))))))))).))..))))))........)--)....))))))))))). ( -25.46)
>DroSim_CAF1 7621 112 + 1
AAUUAUGACCCAAAAUUGCAGUAUACAUUUGUUCGGAGCCUUUGUAGGCUUUUUAUAAA-CUUUUUGUGGGGGCUUAUAUUGCCCUGCUUUUUCGG--UUUUUAUUGUUGGGUCC
......((((((.....((((((.((.(((((..(((((((....)))))))..)))))-.........(((((.......))))).........)--)...)))))))))))). ( -32.90)
>DroEre_CAF1 7021 105 + 1
AAUUAUGACCCAAAAUUGUAUUGUAAAUUUAUUCAGUGCCCUUUUAGGCUUUUAUUA-AGGUUUAUUGU-GGUUUUAUAUUGCUUUGCU-------CCCUUCUAUUGUUGGG-CC
...((.(((((((....((((((..........)))))).....((((((((....)-)))))))))).-)))).))....(((..((.-------..........))..))-). ( -15.90)
>consensus
AAUUAUGACCCAAAAUUGCAGUAUACAUUUGUUCGGUGCCUUUGUAGGCUUUUUAUAAA_CUUUUUUGU_GGGCUUAUAUUGCCCUGCUUUUUCGG__UUUCUAUUGUUGGGUCC
......(((((((........................((((....))))..................(((((((.......)))))))...................))))))). (-18.17 = -19.68 +   1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,089,739 – 15,089,849
Length 110
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 82.79
Mean single sequence MFE -23.06
Consensus MFE -16.01
Energy contribution -17.32
Covariance contribution 1.31
Combinations/Pair 1.07
Mean z-score -3.40
Structure conservation index 0.69
SVM decision value 2.75
SVM RNA-class probability 0.996769
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15089739 110 - 23771897
GGACCCAACAAUAGAAA--CCGAAAAAGCAGGGCAAUAUAAGCCC-ACAAAAAAG-UGUAUAAAAAGCCUA-AAAGGCACCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUU
.(((((((.....(...--.)......((.((((.......))))-.......((-((((((....(((..-...)))..........))))))))))....)))))))...... ( -26.34)
>DroSec_CAF1 7022 112 - 1
GGACCCAACAAUAGAAA--CCGAAAAAGCAGUGCAAUAAAAGCCCCACAAAAAAG-UUUAUAAAAAGCCUACAAAGGCACCGAACAAAUGUAAACUGCAAUUUUGGGUCAUAAUU
.(((((((.....(...--.)......((((((((....((((...........)-))).......((((....))))..........)))..)))))....)))))))...... ( -22.30)
>DroSim_CAF1 7621 112 - 1
GGACCCAACAAUAAAAA--CCGAAAAAGCAGGGCAAUAUAAGCCCCCACAAAAAG-UUUAUAAAAAGCCUACAAAGGCUCCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUU
.((((((((........--..).....((((.(((.(((((((...........)-))))))...(((((....))))).........)))...))))....)))))))...... ( -25.40)
>DroEre_CAF1 7021 105 - 1
GG-CCCAACAAUAGAAGGG-------AGCAAAGCAAUAUAAAACC-ACAAUAAACCU-UAAUAAAAGCCUAAAAGGGCACUGAAUAAAUUUACAAUACAAUUUUGGGUCAUAAUU
((-(((((......((((.-------...................-........)))-).......((((....))))........................)))))))...... ( -18.19)
>consensus
GGACCCAACAAUAGAAA__CCGAAAAAGCAGGGCAAUAUAAGCCC_ACAAAAAAG_UUUAUAAAAAGCCUACAAAGGCACCGAACAAAUGUAUACUGCAAUUUUGGGUCAUAAUU
.(((((((......................((((.......)))).....................((((....))))........................)))))))...... (-16.01 = -17.32 +   1.31)

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 11:51:57 2006