Locus 5684

Sequence ID 3R_DroMel_CAF1
Location 14,909,753 – 14,909,845
Length 92
Max. P 0.871846
window9292 window9293

overview

Window 2

Location 14,909,753 – 14,909,845
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 82.42
Mean single sequence MFE -17.98
Consensus MFE -12.68
Energy contribution -13.08
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.71
SVM decision value 0.52
SVM RNA-class probability 0.768713
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14909753 92 + 27905053
CGAAAAAGAAAAGAAGAAAUUGUGGCAGCAACAACAGCAAAUGCAACAGCAACGGCAACUGCAUGCCAUCCGUCUAUCGAAUGCCACUAUCA
...............((....((((((((.......))...(((....)))..((((......))))..............))))))..)). ( -18.60)
>DroSec_CAF1 36979 92 + 1
CGAAAAAGAAAAGAAGAAAUUGUGGCAGCAGCAACAGCAAAUGCAACAGCAACGGCAACUGCAUGCCAUCCGUCUAUCGAAUGCCACUAUCA
...............((....((((((((((((...((...(((....)))...))...))).)))....((.....))..))))))..)). ( -20.90)
>DroSim_CAF1 36935 74 + 1
CGAAAAGGAAAAGAAGAAAUUGUGGC------------------AACAGCAACGGCAACUGCAUGCCAUCCGUCUAUCGAAUGCCACUAUCA
......((....(((((....(((((------------------(...(((..(....)))).))))))...))).)).....))....... ( -15.90)
>DroEre_CAF1 36385 77 + 1
CGAAAAAGAAAA---GAAAUUGUAGCAACAGCAACGG------C------AACGGCAACUACAAGCCAUCCGUCUAUCGAAUGCCACUAUCA
.((.........---......((.((....)).))((------(------(..(((........)))...((.....))..))))....)). ( -13.60)
>DroYak_CAF1 43354 83 + 1
CGAAAAAGAAAA---GAAAUUGUGGCAACAGCAACGG------CAACGGCAACGGCAACUGCAAGCCAUCCGUCUAUCGAAUGCCACUAUCA
............---((....((((((........((------(..((....))((....))..)))...((.....))..))))))..)). ( -20.90)
>consensus
CGAAAAAGAAAAGAAGAAAUUGUGGCAACAGCAACAG______CAACAGCAACGGCAACUGCAUGCCAUCCGUCUAUCGAAUGCCACUAUCA
...............((....((((((..........................(((........)))...((.....))..))))))..)). (-12.68 = -13.08 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,909,753 – 14,909,845
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 82.42
Mean single sequence MFE -24.52
Consensus MFE -16.68
Energy contribution -16.52
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.68
SVM decision value 0.87
SVM RNA-class probability 0.871846
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14909753 92 - 27905053
UGAUAGUGGCAUUCGAUAGACGGAUGGCAUGCAGUUGCCGUUGCUGUUGCAUUUGCUGUUGUUGCUGCCACAAUUUCUUCUUUUCUUUUUCG
.....((((((..((((((.((((((.((.(((((.......)))))))))))))))))))....))))))..................... ( -27.80)
>DroSec_CAF1 36979 92 - 1
UGAUAGUGGCAUUCGAUAGACGGAUGGCAUGCAGUUGCCGUUGCUGUUGCAUUUGCUGUUGCUGCUGCCACAAUUUCUUCUUUUCUUUUUCG
.....((((((((((.....)))))((((.((((..((...(((....)))...))..)))))))))))))..................... ( -27.40)
>DroSim_CAF1 36935 74 - 1
UGAUAGUGGCAUUCGAUAGACGGAUGGCAUGCAGUUGCCGUUGCUGUU------------------GCCACAAUUUCUUCUUUUCCUUUUCG
.....((((((....((((...(((((((......))))))).)))))------------------)))))..................... ( -21.20)
>DroEre_CAF1 36385 77 - 1
UGAUAGUGGCAUUCGAUAGACGGAUGGCUUGUAGUUGCCGUU------G------CCGUUGCUGUUGCUACAAUUUC---UUUUCUUUUUCG
.....((((((..((...((((((((((........))))).------.------)))))..)).))))))......---............ ( -21.30)
>DroYak_CAF1 43354 83 - 1
UGAUAGUGGCAUUCGAUAGACGGAUGGCUUGCAGUUGCCGUUGCCGUUG------CCGUUGCUGUUGCCACAAUUUC---UUUUCUUUUUCG
.....((((((..((((.((((((((((........)))))..))))).------..))))....))))))......---............ ( -24.90)
>consensus
UGAUAGUGGCAUUCGAUAGACGGAUGGCAUGCAGUUGCCGUUGCUGUUG______CCGUUGCUGCUGCCACAAUUUCUUCUUUUCUUUUUCG
.....((((((((((.....)))))(((........)))...........................)))))..................... (-16.68 = -16.52 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:41 2006