Locus 1994

Sequence ID 3L_DroMel_CAF1
Location 5,470,082 – 5,470,222
Length 140
Max. P 0.854391
window3122 window3123

overview

Window 2

Location 5,470,082 – 5,470,191
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 82.52
Mean single sequence MFE -21.30
Consensus MFE -13.78
Energy contribution -14.86
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -1.91
Structure conservation index 0.65
SVM decision value 0.34
SVM RNA-class probability 0.696553
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5470082 109 - 23771897
GGUUAUCCCCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGCGGUAGAACCCACCUUGCGUAACUUUUGGCCCACCCAC
...............(((......((((((.(((((((............)))))))...............(((.......)))))))))......)))......... ( -21.50)
>DroSec_CAF1 31682 100 - 1
--------CCCUUCCCCAUUUAUAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGCGGUAGAACACACCUUGCGUAACUUUUGGC-CACCCAC
--------.......(((......((((((.(((((((............)))))))...............(((.......)))))))))......))).-....... ( -21.50)
>DroSim_CAF1 33229 100 - 1
--------CCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGCGGUAGAACACACCUUGCGUAACUUUUGGC-CACCCAC
--------.......(((......((((((.(((((((............)))))))...............(((.......)))))))))......))).-....... ( -21.50)
>DroEre_CAF1 31172 105 - 1
AGUUAC--CCCUUC-CCAUUUUCUGCACAACCUGGCCAAUACCUCAGACGUGGCCAGCACCUU-CAUAUAGCGGUAGAACCCGCCUUGCGUAACUGCCGCCUCACCCAC
......--......-................(((((((...(....)...)))))))......-......(((((((....(((...)))...)))))))......... ( -23.90)
>DroYak_CAF1 19147 97 - 1
AGUUAU--CCCUUCCCCAUAUCCAGCACAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUU-CCGAAAG---------UUACCUAGCGUAACUAUGGCCCCACCCAC
......--.......((((............(((((((............)))))))......-.....((---------((((.....)))))))))).......... ( -18.10)
>consensus
_GUUA___CCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGCGGUAGAACACACCUUGCGUAACUUUUGGC_CACCCAC
........................((((((.(((((((............)))))))...............(((.......))))))))).................. (-13.78 = -14.86 +   1.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,470,119 – 5,470,222
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -25.14
Consensus MFE -17.08
Energy contribution -18.28
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.68
SVM decision value 0.80
SVM RNA-class probability 0.854391
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5470119 103 - 23771897
CAUUGUUCC---------CUGGUUGCAAGCUUAAAGGCUAGGUUAUCCCCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGC
...(((...---------..((((((..(((((((((..(((.......)))...)).)))).)))))))))((((((............)))))))))............. ( -24.10)
>DroSec_CAF1 31718 94 - 1
CAUCGUGCU---------CUGGUUGCAAGCUUAAAGGCU---------CCCUUCCCCAUUUAUAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGC
....((((.---------..((((((..(((((((((..---------.......)).)))).)))))))))((((((............))))))))))............ ( -25.70)
>DroSim_CAF1 33265 94 - 1
CAUCGUGCU---------CUGGUUGCAAGCUUUAAGGCU---------CCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGC
....((((.---------..((((((..(((.((((...---------..........)))).)))))))))((((((............))))))))))............ ( -24.82)
>DroEre_CAF1 31209 108 - 1
CAUCGUGCUUUUCGUUCCCUGGUUGCAAGCUUAAAGGAUCAGUUAC--CCCUUC-CCAUUUUCUGCACAACCUGGCCAAUACCUCAGACGUGGCCAGCACCUU-CAUAUAGC
....((((............(((((...((..((((((........--....))-)...)))..)).)))))((((((...(....)...))))))))))...-........ ( -21.70)
>DroYak_CAF1 19176 108 - 1
CAUCGUACUUUUGGCCUCCUGGGUGGAAGCUUAAAGGAUCAGUUAU--CCCUUCCCCAUAUCCAGCACAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUU-CCGAAAG-
.......(((((((....(((((((((((......((((.....))--)))))))....))))))......(((((((............)))))))......-)))))))- ( -29.40)
>consensus
CAUCGUGCU_________CUGGUUGCAAGCUUAAAGGCU__GUUA___CCCUUCCCCAUUUACAGCGCAACCUGGCCAAUACCUCAGACAUGGCCAGCACCUUUCAUAUAGC
....((((............((((((..(((..((((............))))..........)))))))))((((((............))))))))))............ (-17.08 = -18.28 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:01 2006