Locus 7924

Sequence ID X_DroMel_CAF1
Location 19,730,208 – 19,730,301
Length 93
Max. P 0.828139
window13003 window13004

overview

Window 3

Location 19,730,208 – 19,730,301
Length 93
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 75.28
Mean single sequence MFE -26.84
Consensus MFE -18.66
Energy contribution -19.47
Covariance contribution 0.81
Combinations/Pair 1.10
Mean z-score -1.27
Structure conservation index 0.70
SVM decision value 0.70
SVM RNA-class probability 0.828139
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19730208 93 + 22224390
UU--CCU-UUGGGGCGUGGCACAU-GUUGCGUGCGCCUAAUUACGCGUAAUUAUUCACUUAGUGUGUUAUGACAACAGCAG-GAAAAGGAGGGGAACA-----
((--(((-(((..(((((((((((-((((((((..........))))))))..........)))))))))).)..))).))-))).............----- ( -25.80)
>DroPse_CAF1 30102 87 + 1
UUUGUCU-UGGGGGCGUGGCACAU-GUUGCGUGCACUUAAUGAUGCGUAAUUAUUCACUUAGUUGGUUAUGCCACAAAAA-------UGAUGACGA-------
.(((((.-...(.(((..((....-))..))).)..........(((((((((..........)))))))))........-------....)))))------- ( -20.50)
>DroSec_CAF1 26047 93 + 1
UU--CCU-UUGGGGCGUGGCACAU-GUUGCGUGCGCCUAAUUCCGCGUAAUUAUUCACUUAGUGUGUUAUGCCAACAGCAG-AAAGAGGAGGGCAACA-----
((--(((-((..((((((((((((-((((((((..........))))))))..........))))))))))))........-..)))))))(....).----- ( -29.10)
>DroSim_CAF1 2952 93 + 1
UU--CCU-UUGGGGCGUGGCACAU-GUUGCGUGCGCCUAAUUACGCGUAAUUAUUCACUUAGUGUGUUAUGCCAACAGCAG-AAAGAGGAGGGCAACA-----
((--(((-((..((((((((((((-((((((((..........))))))))..........))))))))))))........-..)))))))(....).----- ( -29.50)
>DroYak_CAF1 23012 98 + 1
UU--CCUUUUGGGGCGUGGCACAU-GUUGCGUGCGCCUAAUUACGCGUAAUUAUUCACUUAGUGUGUUAUGCCAACAGCAG-C-AGAGAAGGGGAACAAAAAA
((--((((((..((((((((((((-((((((((..........))))))))..........))))))))))))........-.-...))))))))........ ( -29.04)
>DroMoj_CAF1 32724 80 + 1
--------AGGGGGCGUGUCACGUUUUUGCGUGCACUUAAUUGUGCGUAAUUAUUCACUUUAGUUGUUAUGCCAACGAGUGGC-GGCCC--------------
--------...((((.((((((((..(((((..((......))..)))))..))........((((......))))..)))))-)))))-------------- ( -27.10)
>consensus
UU__CCU_UUGGGGCGUGGCACAU_GUUGCGUGCGCCUAAUUACGCGUAAUUAUUCACUUAGUGUGUUAUGCCAACAGCAG_A_AGAGGAGGGCAACA_____
............((((((((((((.((((((((..........))))))))..........)))))))))))).............................. (-18.66 = -19.47 +   0.81)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 19,730,208 – 19,730,301
Length 93
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 75.28
Mean single sequence MFE -21.06
Consensus MFE -12.64
Energy contribution -12.75
Covariance contribution 0.11
Combinations/Pair 1.13
Mean z-score -1.31
Structure conservation index 0.60
SVM decision value -0.05
SVM RNA-class probability 0.507368
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19730208 93 - 22224390
-----UGUUCCCCUCCUUUUC-CUGCUGUUGUCAUAACACACUAAGUGAAUAAUUACGCGUAAUUAGGCGCACGCAAC-AUGUGCCACGCCCCAA-AGG--AA
-----........((((((..-..((...........(((.....)))..((((((....))))))((((((......-.))))))..))...))-)))--). ( -19.10)
>DroPse_CAF1 30102 87 - 1
-------UCGUCAUCA-------UUUUUGUGGCAUAACCAACUAAGUGAAUAAUUACGCAUCAUUAAGUGCACGCAAC-AUGUGCCACGCCCCCA-AGACAAA
-------..(((....-------....(((((((((.........((((....))))((((......)))).......-.)))))))))......-.)))... ( -20.16)
>DroSec_CAF1 26047 93 - 1
-----UGUUGCCCUCCUCUUU-CUGCUGUUGGCAUAACACACUAAGUGAAUAAUUACGCGGAAUUAGGCGCACGCAAC-AUGUGCCACGCCCCAA-AGG--AA
-----........((((..((-(((((((((...)))))......((((....))))))))))...((((((......-.)))))).........-)))--). ( -20.90)
>DroSim_CAF1 2952 93 - 1
-----UGUUGCCCUCCUCUUU-CUGCUGUUGGCAUAACACACUAAGUGAAUAAUUACGCGUAAUUAGGCGCACGCAAC-AUGUGCCACGCCCCAA-AGG--AA
-----........((((....-..((.((.((((((.(((.....))).........((((......)))).......-.)))))))))).....-)))--). ( -21.40)
>DroYak_CAF1 23012 98 - 1
UUUUUUGUUCCCCUUCUCU-G-CUGCUGUUGGCAUAACACACUAAGUGAAUAAUUACGCGUAAUUAGGCGCACGCAAC-AUGUGCCACGCCCCAAAAGG--AA
...........((((...(-(-..((.((.((((((.(((.....))).........((((......)))).......-.))))))))))..)).))))--.. ( -21.50)
>DroMoj_CAF1 32724 80 - 1
--------------GGGCC-GCCACUCGUUGGCAUAACAACUAAAGUGAAUAAUUACGCACAAUUAAGUGCACGCAAAAACGUGACACGCCCCCU--------
--------------((((.-((((.....))))............(((.........((((......)))).(((......))).)))))))...-------- ( -23.30)
>consensus
_____UGUUGCCCUCCUCU_G_CUGCUGUUGGCAUAACACACUAAGUGAAUAAUUACGCGUAAUUAGGCGCACGCAAC_AUGUGCCACGCCCCAA_AGG__AA
.............................(((((((.........((((....))))((((......)))).........)))))))................ (-12.64 = -12.75 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:57 2006