Locus 5986

Sequence ID 3L_DroMel_CAF1
Location 15,992,495 – 15,992,596
Length 101
Max. P 0.941739
window9571 window9572

overview

Window 1

Location 15,992,495 – 15,992,596
Length 101
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -21.25
Consensus MFE -19.12
Energy contribution -19.38
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.90
SVM decision value 0.95
SVM RNA-class probability 0.888495
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15992495 101 + 23771897
AGGUGGAAA-AAAG-------AAGAAAAUAAGGCAAAAUAUUAAUAAGCAGUGCCCGCAAUUAAUAGCGCAACUUAAGACUCUAUAUAGGGUAAUUAAGCGGCGCUUGU
.........-....-------...........((((..(((((((..((.......)).)))))))((((..(((((.(((((....)))))..)))))..)))))))) ( -20.30)
>DroVir_CAF1 2854 106 + 1
AAGCAGAAA-AGAGUCGCUACAAGCC--AAAAGCAAAAUAUUAAUAAGCAGUGCCCGCAAUUAAUAGCGCAACUUAAGACGCUAUAUAGGGUAAUUAAGCGGCGCUUGU
........(-((.((((((....((.--....)).................(((((.......(((((((.......).))))))...)))))....)))))).))).. ( -24.10)
>DroSim_CAF1 465 102 + 1
AGGUGGAAAAAAAG-------AAGAAAAUAAGGCAAAAUAUUAAUAAGCAGUGCCCGCAAUUAAUAGCGCAACUUAAGACUCUAUAUAGGGUAAUUAAGCGGCGCUUGU
..............-------...........((((..(((((((..((.......)).)))))))((((..(((((.(((((....)))))..)))))..)))))))) ( -20.30)
>DroYak_CAF1 16053 101 + 1
AGGUGGAAA-AAAG-------AAGAAAAUAAGGCAAAAUAUUAAUAAGCAGUGCCCGCAAUUAAUAGCGCAACUUAAGACUCUAUAUAGGGUAAUUAAGCGGCGCUUGU
.........-....-------...........((((..(((((((..((.......)).)))))))((((..(((((.(((((....)))))..)))))..)))))))) ( -20.30)
>consensus
AGGUGGAAA_AAAG_______AAGAAAAUAAGGCAAAAUAUUAAUAAGCAGUGCCCGCAAUUAAUAGCGCAACUUAAGACUCUAUAUAGGGUAAUUAAGCGGCGCUUGU
................................((((..(((((((..((.......)).)))))))((((..(((((.(((((....)))))..)))))..)))))))) (-19.12 = -19.38 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 15,992,495 – 15,992,596
Length 101
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 90.95
Mean single sequence MFE -19.63
Consensus MFE -18.45
Energy contribution -18.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.94
SVM decision value 1.32
SVM RNA-class probability 0.941739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15992495 101 - 23771897
ACAAGCGCCGCUUAAUUACCCUAUAUAGAGUCUUAAGUUGCGCUAUUAAUUGCGGGCACUGCUUAUUAAUAUUUUGCCUUAUUUUCUU-------CUUU-UUUCCACCU
...(((((.((((((..((.((....)).)).)))))).)))))((((((.((((...))))..))))))..................-------....-......... ( -18.50)
>DroVir_CAF1 2854 106 - 1
ACAAGCGCCGCUUAAUUACCCUAUAUAGCGUCUUAAGUUGCGCUAUUAAUUGCGGGCACUGCUUAUUAAUAUUUUGCUUUU--GGCUUGUAGCGACUCU-UUUCUGCUU
(((((((((.(.((((((......(((((((........))))))))))))).))))...((.............))....--.))))))(((((....-..)).))). ( -23.02)
>DroSim_CAF1 465 102 - 1
ACAAGCGCCGCUUAAUUACCCUAUAUAGAGUCUUAAGUUGCGCUAUUAAUUGCGGGCACUGCUUAUUAAUAUUUUGCCUUAUUUUCUU-------CUUUUUUUCCACCU
...(((((.((((((..((.((....)).)).)))))).)))))((((((.((((...))))..))))))..................-------.............. ( -18.50)
>DroYak_CAF1 16053 101 - 1
ACAAGCGCCGCUUAAUUACCCUAUAUAGAGUCUUAAGUUGCGCUAUUAAUUGCGGGCACUGCUUAUUAAUAUUUUGCCUUAUUUUCUU-------CUUU-UUUCCACCU
...(((((.((((((..((.((....)).)).)))))).)))))((((((.((((...))))..))))))..................-------....-......... ( -18.50)
>consensus
ACAAGCGCCGCUUAAUUACCCUAUAUAGAGUCUUAAGUUGCGCUAUUAAUUGCGGGCACUGCUUAUUAAUAUUUUGCCUUAUUUUCUU_______CUUU_UUUCCACCU
...(((((.((((((..((.((....)).)).)))))).)))))((((((.((((...))))..))))))....................................... (-18.45 = -18.45 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:03 2006