Locus 2809

Sequence ID 3R_DroMel_CAF1
Location 7,515,816 – 7,516,008
Length 192
Max. P 0.960135
window4542 window4543 window4544

overview

Window 2

Location 7,515,816 – 7,515,906
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 80.37
Mean single sequence MFE -21.84
Consensus MFE -16.33
Energy contribution -18.39
Covariance contribution 2.06
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.75
SVM decision value 1.51
SVM RNA-class probability 0.960135
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7515816 90 + 27905053
UGGUCGUGAUGCAAAAGCCACAUUCAUGACCGAACGACUUAAAAAAAAGCGUCGUAUCAGUCGUUCUAAACAAACGUCUAGAUCAUGCUG
.((((((((.((....)).....))))))))................(((((.(.(((((.((((.......)))).)).))))))))). ( -22.30)
>DroSec_CAF1 11467 89 + 1
UGGUCGUGAUGCAAGAACCACAUUCAUGACCGAACGAAAUAAA-AAAAGCGUCUAAUCAGCCGUUCUAGACACACGUCUAGAUCUUGCUG
.((((((((..............))))))))............-.............((((...(((((((....)))))))....)))) ( -24.54)
>DroSim_CAF1 11970 90 + 1
UGGUCGUGAUGCAAGAACCACAUUCAUGACCGAACGACUUAAAAAAAAGCGUCUAAUCAGCCGUUCUAGACACACGUCUAGAUCUUGCUG
.((((((((..............))))))))((.((.(((......)))))))....((((...(((((((....)))))))....)))) ( -26.94)
>DroEre_CAF1 11544 70 + 1
------------------CACAUGCACGCCCGAACGACAA-GAAAAAAGCGUCUAAUCAGCCGUUCUAGACA-ACGUCUAGAUCUUGCUG
------------------.......((((...........-.......)))).....((((...(((((((.-..)))))))....)))) ( -13.57)
>consensus
UGGUCGUGAUGCAAGAACCACAUUCAUGACCGAACGACAUAAAAAAAAGCGUCUAAUCAGCCGUUCUAGACACACGUCUAGAUCUUGCUG
.((((((((..............))))))))..........................((((...(((((((....)))))))....)))) (-16.33 = -18.39 +   2.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,515,816 – 7,515,906
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 80.37
Mean single sequence MFE -24.75
Consensus MFE -18.36
Energy contribution -20.18
Covariance contribution 1.81
Combinations/Pair 1.14
Mean z-score -1.80
Structure conservation index 0.74
SVM decision value 0.66
SVM RNA-class probability 0.815967
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7515816 90 - 27905053
CAGCAUGAUCUAGACGUUUGUUUAGAACGACUGAUACGACGCUUUUUUUUAAGUCGUUCGGUCAUGAAUGUGGCUUUUGCAUCACGACCA
...((((((((((((....)))))((((((((...................)))))))))))))))..((((((....))..)))).... ( -24.11)
>DroSec_CAF1 11467 89 - 1
CAGCAAGAUCUAGACGUGUGUCUAGAACGGCUGAUUAGACGCUUUU-UUUAUUUCGUUCGGUCAUGAAUGUGGUUCUUGCAUCACGACCA
((((....(((((((....)))))))...)))).............-............((((.(((.((..(...)..))))).)))). ( -24.80)
>DroSim_CAF1 11970 90 - 1
CAGCAAGAUCUAGACGUGUGUCUAGAACGGCUGAUUAGACGCUUUUUUUUAAGUCGUUCGGUCAUGAAUGUGGUUCUUGCAUCACGACCA
((((....(((((((....)))))))...))))....(((((((......))).)))).((((.(((.((..(...)..))))).)))). ( -28.60)
>DroEre_CAF1 11544 70 - 1
CAGCAAGAUCUAGACGU-UGUCUAGAACGGCUGAUUAGACGCUUUUUUC-UUGUCGUUCGGGCGUGCAUGUG------------------
..((....(((((((..-.)))))))(((.((((...((((........-.))))..)))).))))).....------------------ ( -21.50)
>consensus
CAGCAAGAUCUAGACGUGUGUCUAGAACGGCUGAUUAGACGCUUUUUUUUAAGUCGUUCGGUCAUGAAUGUGGUUCUUGCAUCACGACCA
..(((((((((((((....)))))))..((((((...(((............)))..))))))...........)))))).......... (-18.36 = -20.18 +   1.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,515,906 – 7,516,008
Length 102
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 70.62
Mean single sequence MFE -22.94
Consensus MFE -12.53
Energy contribution -13.73
Covariance contribution 1.20
Combinations/Pair 1.29
Mean z-score -1.58
Structure conservation index 0.55
SVM decision value 0.18
SVM RNA-class probability 0.622106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7515906 102 + 27905053
--------CUUGAAACCUAAUGAUGAUCAGCACUGAGCUUUUUUUUGCAGUUUCAUUGUUACAAUGGCUUU--UUCAGCAAUGACUUGCAGC-CUUGGUUCAACAAUUAUCUG
--------.(((((.(((((..(((((((....)))((........))....))))..)))....((((..--.(((....))).....)))-)..))))))).......... ( -20.00)
>DroSec_CAF1 11556 96 + 1
--------CUUGAACUCUAAU---GAUCAGCUCUGAGCUUUUUUUUGCAGGUUCAUUGUUACGAUGACUUU--UUUAGCAAUGACUUGCAGC-CUUGGUUCA---AUUAUCUG
--------.(((((((.....---....(((.....))).....((((((((.((((((((.((......)--).)))))))))))))))).-...))))))---)....... ( -25.30)
>DroSim_CAF1 12060 96 + 1
--------CUUGAACUCUAAU---GAUCAGCGCUGAGCUUUUUUUUGCAGGUUCAUUGUUACGAUGACUUU--UUGAGCAAUGACUUGCAGC-CUUGGUUCA---AUUAUCUG
--------.(((((((.....---....(((.....))).....((((((((.(((((((.(((.......--)))))))))))))))))).-...))))))---)....... ( -25.70)
>DroYak_CAF1 11545 96 + 1
--------ACUGAACUUCAGU---GAUCACCUCUGUGCUUUUUUUUGCAGGCUCACUGUUACGGCGACUUU--CUCAGCAAUGACUGGCAGC-CUUGACUUA---AUUAUCUG
--------..........(((---((...(((....((........))))).)))))((((.(((..((..--.(((....)))..))..))-).))))...---........ ( -19.30)
>DroAna_CAF1 11683 105 + 1
UUUUGAAUCUCCAAACUUGCU---AAUCAAGUUUGUAUUGCUUUGUGUUAGUUAAUUAUUACG--GACUGCAAGUAAUCGAUGACUGGCAAAAAGUGGGUUA---UUUAUCUC
.....(((((.((((((((..---...))))))))....(((((.(((((((((.(.(((((.--........))))).).))))))))).)))))))))).---........ ( -24.40)
>consensus
________CUUGAACUCUAAU___GAUCAGCUCUGAGCUUUUUUUUGCAGGUUCAUUGUUACGAUGACUUU__UUCAGCAAUGACUUGCAGC_CUUGGUUCA___AUUAUCUG
........................(((......((((((.....(((((((.((((((((................))))))))))))))).....))))))......))).. (-12.53 = -13.73 +   1.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:12 2006