Locus 1930

Sequence ID 2L_DroMel_CAF1
Location 5,234,816 – 5,234,912
Length 96
Max. P 0.998205
window3118 window3119

overview

Window 8

Location 5,234,816 – 5,234,912
Length 96
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -20.41
Consensus MFE -17.88
Energy contribution -18.40
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -3.41
Structure conservation index 0.88
SVM decision value 3.03
SVM RNA-class probability 0.998205
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5234816 96 + 22407834
U--------AAGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCAC----AC--AAAAAGGCAUAAAAUAUGUGCG
.--------..((((((.(((..((((.((((.............)))).))))..)))..((....))...))))))..----..--......(((((.....))))). ( -21.72)
>DroSec_CAF1 12054 100 + 1
U--------AAGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCACACACAC--AAAAAGGCAUAAAAUAUGUGCG
.--------..((((((.(((..((((.((((.............)))).))))..)))..((....))...))))))........--......(((((.....))))). ( -21.72)
>DroSim_CAF1 12940 100 + 1
U--------AAGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCACACACAC--AAAAAGGCAUAAAAUAUGUGCG
.--------..((((((.(((..((((.((((.............)))).))))..)))..((....))...))))))........--......(((((.....))))). ( -21.72)
>DroEre_CAF1 4717 96 + 1
U--------AGGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCAC----AC--AAAAAGACAUAAAAUAUGUGCG
.--------..((((((.(((..((((.((((.............)))).))))..)))..((....))...))))))..----..--......(((((...)))))... ( -18.32)
>DroYak_CAF1 13999 96 + 1
U--------AAGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCAC----AC--AAAAGGGCAUAAAAUAUGUGCG
.--------..((((((.(((..((((.((((.............)))).))))..)))..((....))...))))))..----..--......(((((.....))))). ( -21.72)
>DroPer_CAF1 3296 110 + 1
CCAGGUCCCAAAAUCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAUGUUGGGCUCACACACAAAAAAAGGCAUAAAAUAUGGGCA
....((((.....(((..(((..((((.((((.............)))).))))..)))..))).....(((((..(((..............)))....))))))))). ( -17.26)
>consensus
U________AAGCCCAAAUCAAAUGCUCAGAUGCAUAUCAAAAUAAUCUAAGCAAAUGAAAUGACAACAAAGUUGGGCAC____AC__AAAAAGGCAUAAAAUAUGUGCG
...........((((...(((..((((.((((.............)))).))))..)))...(((......)))))))................(((((.....))))). (-17.88 = -18.40 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,234,816 – 5,234,912
Length 96
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -27.95
Consensus MFE -20.66
Energy contribution -20.85
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -4.44
Structure conservation index 0.74
SVM decision value 1.54
SVM RNA-class probability 0.962544
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5234816 96 - 22407834
CGCACAUAUUUUAUGCCUUUUU--GU----GUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCUU--------A
.(((((...............)--))----))((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))..--------. ( -26.36)
>DroSec_CAF1 12054 100 - 1
CGCACAUAUUUUAUGCCUUUUU--GUGUGUGUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCUU--------A
((((((((.............)--))))))).((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))..--------. ( -30.42)
>DroSim_CAF1 12940 100 - 1
CGCACAUAUUUUAUGCCUUUUU--GUGUGUGUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCUU--------A
((((((((.............)--))))))).((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))..--------. ( -30.42)
>DroEre_CAF1 4717 96 - 1
CGCACAUAUUUUAUGUCUUUUU--GU----GUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCCU--------A
.(((((...............)--))----))((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))..--------. ( -25.96)
>DroYak_CAF1 13999 96 - 1
CGCACAUAUUUUAUGCCCUUUU--GU----GUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCUU--------A
.(((((...............)--))----))((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))..--------. ( -26.36)
>DroPer_CAF1 3296 110 - 1
UGCCCAUAUUUUAUGCCUUUUUUUGUGUGUGAGCCCAACAUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGAUUUUGGGACCUGG
...(((...((((((((.......).)))))))(((((.......((((..(((..((((((((((((......))).)))))))))..)))..)))).)))))...))) ( -28.20)
>consensus
CGCACAUAUUUUAUGCCUUUUU__GU____GUGCCCAACUUUGUUGUCAUUUCAUUUGCUUAGAUUAUUUUGAUAUGCAUCUGAGCAUUUGAUUUGGGCUU________A
................................((((((...((....))..(((..((((((((((((......))).)))))))))..))).))))))........... (-20.66 = -20.85 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:10 2006