Locus 4819

Sequence ID 3R_DroMel_CAF1
Location 12,596,795 – 12,596,924
Length 129
Max. P 0.843245
window7898 window7899

overview

Window 8

Location 12,596,795 – 12,596,898
Length 103
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.74
Mean single sequence MFE -31.07
Consensus MFE -18.53
Energy contribution -19.07
Covariance contribution 0.53
Combinations/Pair 1.26
Mean z-score -2.73
Structure conservation index 0.60
SVM decision value 0.76
SVM RNA-class probability 0.843245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12596795 103 + 27905053
------AGAGGA-------GGGCUUCGAGCAAAUCGACG---CUUUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAU
------.((((.-------...))))..((((.(((..(---(...((((((((((((((((((..(.....)...)))))))))))))))))).))..))).))))............ ( -30.40)
>DroVir_CAF1 86610 110 + 1
------AGACGCCGGCUCGUGGCAUCAAACAAAUCGGUGG--CGGCGUUUUGUUUACGGCUCUU-UCGAGCUGUAAAAAUGUCGUAAACGCAAUUGUUAUGAAUUGCGGUAAAUUAAAU
------...(((((..(.((........)).)..)))))(--(((((((((...((((((((..-..))))))))))))))))))...(((((((......)))))))........... ( -38.50)
>DroPse_CAF1 82524 110 + 1
CAAGACAGAGAG-------AGCCAUCAAACAAAUCGACGG--CAGUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAU
((.((((.....-------.(((.((.........)).))--)...((((((((((((((((((..(.....)...)))))))))))))))))))))).)).................. ( -28.00)
>DroGri_CAF1 83034 109 + 1
------AGACGGCGGCUCGUGGCAUCAAACAAAUCGACGA--CCGCAUUUUGUUUACGACUUU--UUGAGCUGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGUAAAUUAAAU
------..((.((((.((((((((..........((....--.)).(((((((((((((((((--(((.....)))))).)))))))))))))))))))))).)))).))......... ( -31.20)
>DroAna_CAF1 76919 110 + 1
------AGAGGCGGGC---GGGCGUCAAACAAAUCGACGGCAGUGUGUUUUGUUUACGGCAUUUGUCGAGUUGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAU
------.((((((.((---.(.((((.........)))).).)).))))))(((((((((((((............)))))))))))))....((((..(.....)..))))....... ( -30.30)
>DroPer_CAF1 87983 110 + 1
CAAGACAGAAAG-------AGCCAUCAAACAAAUCGACGG--CAGUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAU
((.((((.....-------.(((.((.........)).))--)...((((((((((((((((((..(.....)...)))))))))))))))))))))).)).................. ( -28.00)
>consensus
______AGAGGG_______AGGCAUCAAACAAAUCGACGG__CAGUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAU
.....................((((((((((.....((......))((((((((((((((((((..(.....)...)))))))))))))))))))))).)))..)))............ (-18.53 = -19.07 +   0.53)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 12,596,821 – 12,596,924
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.10
Mean single sequence MFE -28.13
Consensus MFE -20.62
Energy contribution -20.15
Covariance contribution -0.47
Combinations/Pair 1.24
Mean z-score -2.64
Structure conservation index 0.73
SVM decision value 0.53
SVM RNA-class probability 0.771357
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12596821 103 + 27905053
---CUUUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAUAAACAUCAAAUGCCAAACGC-UUCUGU-------------
---....((((((((((((((((((..(.....)...)))))))))))))))))).............((((..................))))......-......------------- ( -23.97)
>DroVir_CAF1 86643 113 + 1
G--CGGCGUUUUGUUUACGGCUCUU-UCGAGCUGUAAAAAUGUCGUAAACGCAAUUGUUAUGAAUUGCGGUAAAUUAAAUAAACAUCAAAUGCCAAACGCCUUUUGUGUCUGCCAG----
(--(((((((((...((((((((..-..))))))))))))))))))...(((((((......))))))).....................((.((.((((.....)))).)).)).---- ( -33.00)
>DroPse_CAF1 82556 104 + 1
G--CAGUGUUUUGUUUACGGCAUUUGUCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAUAAACAUCAAAUGCCAAACGC-UUCUGC-------------
(--((((((((((((((((((((((..(.....)...))))))))))))))))))........)))))((((..................))))....((-....))------------- ( -27.77)
>DroGri_CAF1 83067 115 + 1
A--CCGCAUUUUGUUUACGACUUU--UUGAGCUGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGUAAAUUAAAUAAACAUCAAAUGCCAAAUGU-UUUUGUGUCUGUCCGCCCU
(--(((((((((((((((((((((--(((.....)))))).)))))))))))))...........)))))).......(((.(((.((((.((.....))-.))))))).)))....... ( -27.40)
>DroWil_CAF1 53440 103 + 1
G--UGGCAUUUUGUUUACGGCAUUU-UCAAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAUAAACAUCAAAUGCCAAAUGC-UUAUGU-------------
.--((((((((((((((((((((((-(.........))))))))))))))))))((((..(.....)..)))).................))))).....-......------------- ( -27.20)
>DroAna_CAF1 76949 106 + 1
GCAGUGUGUUUUGUUUACGGCAUUUGUCGAGUUGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAUAAACAUCAAAUGCCAAACGC-UUCUGC-------------
((((.((((((((((((((((((((............)))))))))))))))................((((..................)))).)))))-..))))------------- ( -29.47)
>consensus
G__CGGCGUUUUGUUUACGGCAUUU_UCGAGUAGUAAAAAUGUCGUAAACGAAAUUGUUAUGAAUUGCGGCAAAUUAAAUAAACAUCAAAUGCCAAACGC_UUCUGU_____________
.....((((((((((((((((((((..(.....)...)))))))))))))).................((((..................)))))))))).................... (-20.62 = -20.15 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:37 2006