Locus 1513

Sequence ID	3R_DroMel_CAF1
Location	4,323,895 – 4,323,989
Length	94
Max. P	0.920669

overview

Window 8

Location	4,323,895 – 4,323,989
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	95.96
Mean single sequence MFE	-23.78
Consensus MFE	-21.00
Energy contribution	-21.40
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.88
SVM decision value	0.50
SVM RNA-class probability	0.758690
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4323895 94 + 27905053
CGACCAACUAACUAACCAUCCAGCCAGCGCAGCUGAAGGUUAUCUAAAAUAUUACCAACUGCCGGCCGCCGCAGGAAUUCAAUGGCUGGUCUGA
....................((((((((.((..(((((((.............)))..((((.((...))))))...)))).))))))).))). ( -24.02)
>DroSec_CAF1 11269 94 + 1
CGACCAACUAACUAACCAUCCAGCCAGCGCAGCUGAAGGUUAUCUAAAAUAUUACCAACUGCCGGUCGCCGCAGGAAUUCAAUGGCUGGUCUGA
....................((((((((.((..(((((((.............)))..((((.((...))))))...)))).))))))).))). ( -24.02)
>DroSim_CAF1 255 94 + 1
CGACGAACUAACUAACCAUCCAGCCAGCGCAGCUGAAGGUUAUCUAAAAUAUUACCAACUGCCGGCCGCCGCAGGAAUUCAAUGGCUGGUCUGA
....................((((((((.((..(((((((.............)))..((((.((...))))))...)))).))))))).))). ( -24.02)
>DroEre_CAF1 11269 94 + 1
CGACCAACUAGCUAACCAACCAGCCAGCCCAGCCGAAGGUUAUCUAAAAUAUUACCAACUGCCGGCCGCCGCAGGAAUUCAAUGGCUGGUCUGA
..........(((........)))(((.(((((((..(((.............)))..((((.((...))))))........))))))).))). ( -25.02)
>DroYak_CAF1 2703 94 + 1
CGACCAACUAACUAACCAUCCAGCCAGCCCAGCUGAAGGUUAUCUAAAAUAUUACCAACUGCCGGCCGCCGCAGCCAUUCAAUGGCUGCUCUGA
....................(((...(((..((.(..(((.............)))..).)).)))....((((((((...)))))))).))). ( -21.82)
>consensus
CGACCAACUAACUAACCAUCCAGCCAGCGCAGCUGAAGGUUAUCUAAAAUAUUACCAACUGCCGGCCGCCGCAGGAAUUCAAUGGCUGGUCUGA
....................((((((((.((..(((((((.............)))..((((.((...))))))...)))).))))))).))). (-21.00 = -21.40 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	4,323,895 – 4,323,989
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	95.96
Mean single sequence MFE	-32.42
Consensus MFE	-28.06
Energy contribution	-28.34
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.66
Structure conservation index	0.87
SVM decision value	1.14
SVM RNA-class probability	0.920669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4323895 94 - 27905053
UCAGACCAGCCAUUGAAUUCCUGCGGCGGCCGGCAGUUGGUAAUAUUUUAGAUAACCUUCAGCUGCGCUGGCUGGAUGGUUAGUUAGUUGGUCG
...(((((((.(((((..(((.((..((((..((((((((...((((...))))....)))))))))))))).)))...)))))..))))))). ( -32.50)
>DroSec_CAF1 11269 94 - 1
UCAGACCAGCCAUUGAAUUCCUGCGGCGACCGGCAGUUGGUAAUAUUUUAGAUAACCUUCAGCUGCGCUGGCUGGAUGGUUAGUUAGUUGGUCG
...(((((((.((((.....((((.(....).))))....))))....(((.((((((((((((.....))))))).))))).)))))))))). ( -30.80)
>DroSim_CAF1 255 94 - 1
UCAGACCAGCCAUUGAAUUCCUGCGGCGGCCGGCAGUUGGUAAUAUUUUAGAUAACCUUCAGCUGCGCUGGCUGGAUGGUUAGUUAGUUCGUCG
.(((.(((((.............(((...)))((((((((...((((...))))....))))))))))))))))(((((.........))))). ( -27.30)
>DroEre_CAF1 11269 94 - 1
UCAGACCAGCCAUUGAAUUCCUGCGGCGGCCGGCAGUUGGUAAUAUUUUAGAUAACCUUCGGCUGGGCUGGCUGGUUGGUUAGCUAGUUGGUCG
...(((((((................(((((((..((((.(((....)))..))))..)))))))((((((((....)))))))).))))))). ( -34.30)
>DroYak_CAF1 2703 94 - 1
UCAGAGCAGCCAUUGAAUGGCUGCGGCGGCCGGCAGUUGGUAAUAUUUUAGAUAACCUUCAGCUGGGCUGGCUGGAUGGUUAGUUAGUUGGUCG
.....((((((((...))))))))..((((((((......(((....)))..((((((((((((.....))))))).)))))....)))))))) ( -37.20)
>consensus
UCAGACCAGCCAUUGAAUUCCUGCGGCGGCCGGCAGUUGGUAAUAUUUUAGAUAACCUUCAGCUGCGCUGGCUGGAUGGUUAGUUAGUUGGUCG
...(((((((.......(..((((.(....).))))..).........(((.((((((((((((.....))))))).))))).)))))))))). (-28.06 = -28.34 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:34 2006