Locus 3315

Sequence ID	2R_DroMel_CAF1
Location	11,299,339 – 11,299,468
Length	129
Max. P	0.874052

overview

Window 4

Location	11,299,339 – 11,299,448
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	72.81
Mean single sequence MFE	-34.44
Consensus MFE	-17.20
Energy contribution	-18.37
Covariance contribution	1.17
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.50
SVM decision value	0.88
SVM RNA-class probability	0.874052
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11299339 109 - 20766785
AGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG--GCACACCUGAGCCCCCGUUCGGACCUCCUUUCGCAU---CAGGUCCC-CCC
(((((((((.....)))))))))....(((((..((((((((...)))))))).)))))(((--((........))))).....((((((..........---.)))))).-... ( -37.80)
>DroVir_CAF1 80895 103 - 1
GGUAGUCGGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAGGGCGCGCAUAAUUUUCGGCCGUACACCUGAGCCUAGC-------CACGUGGCAGG-C--UCAGAGUG-G-G
....(((.........))).....((((((((..((.(((((...))))).)).))))).)))....(((((((((((.((-------(....))))))-)--)))).)))-.-. ( -38.30)
>DroGri_CAF1 65056 92 - 1
GAAAGUCUGAUAAACAGACAAUUUGGCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGGCCGCACACCUGAGCCAAGG-------CACGUGGCAAG----------------
....(((((.....))))).......((((((..((((((((...)))))))).)))))).(((((...(((......)))-------...)))))...---------------- ( -32.00)
>DroWil_CAF1 143928 99 - 1
------CUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUAGG--CCACACCUGAGCCCCGAGU-----CUCCUAGUCUGU---GAGUUUCCGUGU
------..(((..((((((.....((((((((..((((((((...)))))))).))))).))--).......((((.....).-----)))...))))))---..)))....... ( -25.70)
>DroYak_CAF1 88541 112 - 1
AGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG--GCACACCUGAGCCCCCGUUCGGACCUCCUUUCGCACAUCGGAGUACC-CCU
(((((((((.....)))))))))....(((((..((((((((...)))))))).)))))(((--(.....((((((....))))))..((((...........))))..))-)). ( -36.50)
>DroAna_CAF1 80157 104 - 1
AGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG--GCGCACCUGAGCCCGCUUU-----CUCCUUUCCCCUU--UCGGUGCC-C-G
(((((((((.....)))))))))..(((((((..((((((((...)))))))).)))))))(--(.(((((.(((........-----............)--))))))))-)-. ( -36.35)
>consensus
AGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG__GCACACCUGAGCCCCCGUU_____CUCCUUGCACGU___GAGGUGCC_C_G
....(((((.....)))))......(((((((..((((((((...)))))))).)))))))...................................................... (-17.20 = -18.37 +   1.17)

alignment

secondary structure

dotplot

Window 5

Location	11,299,375 – 11,299,468
Length	93
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.16
Mean single sequence MFE	-32.56
Consensus MFE	-16.38
Energy contribution	-17.13
Covariance contribution	0.75
Combinations/Pair	1.04
Mean z-score	-1.95
Structure conservation index	0.50
SVM decision value	0.54
SVM RNA-class probability	0.775514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11299375 93 - 20766785
---------------ACUGACUGACUGGGCC-----UGCCAGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG--GCACACCUGAG
---------------...........(((..-----(((((((((((((.....)))))))))..(((((((..((((((((...)))))))).))))))))--)))..)))... ( -36.70)
>DroVir_CAF1 80923 100 - 1
---------------GUCGACUGACUGGGCUGCCGGGGCUGGUAGUCGGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAGGGCGCGCAUAAUUUUCGGCCGUACACCUGAG
---------------.(((((((.(..(.((....)).)..)))))))).....(((.......((((((((..((.(((((...))))).)).))))).))).......))).. ( -27.74)
>DroPse_CAF1 93181 107 - 1
CCGACAGGCAGACGGUCUGACUGACUGGGCC-----UGCCAGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUG-G--GCACACCUGAG
..(.(((((...(((((.....))))).)))-----)).)(((((((((.....)))))))))(((((((((..((((((((...)))))))).))))).-)--)))........ ( -43.50)
>DroGri_CAF1 65073 91 - 1
---------------GGCGACUGACUGAG---------CUGAAAGUCUGAUAAACAGACAAUUUGGCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGGCCGCACACCUGAG
---------------(((..((.(((..(---------(..((.(((((.....)))))..))..))..)))))((((((((...))))))))........)))........... ( -27.80)
>DroWil_CAF1 143960 78 - 1
---------------CUC----GACUGAGC----------------CUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUAGG--CCACACCUGAG
---------------(((----(..((.((----------------((((...............((.....))((((((((...))))))))....)))))--)..))..)))) ( -20.40)
>DroPer_CAF1 92464 107 - 1
CCGACAGACAGACGGUAUGACUGACUGAGCC-----UGCCAGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUG-G--GCACACCUGAG
....(((.(((.(((.....))).))).(((-----.((.(((((((((.....))))))))).))((((((..((((((((...)))))))).))))))-)--))....))).. ( -39.20)
>consensus
_______________GCCGACUGACUGAGCC_____UGCCAGUUGUCUGAUAAACAGACAAUUUGCCAAAGUGGAUACGUGCAUGGCGCGUAUAAUUUUGGG__GCACACCUGAG
........................((.((...............(((((.....))))).......((((((..((((((((...)))))))).))))))..........)).)) (-16.38 = -17.13 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:31 2006