Locus 4260

Sequence ID	X_DroMel_CAF1
Location	11,190,841 – 11,191,001
Length	160
Max. P	0.845670

overview

Window 1

Location	11,190,841 – 11,190,961
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-41.85
Consensus MFE	-36.99
Energy contribution	-38.92
Covariance contribution	1.94
Combinations/Pair	1.05
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	0.12
SVM RNA-class probability	0.595454
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11190841 120 + 22224390
CGGAUCACGCAGAUCGUUUAGCAACUUGGUCAGAUACGGCGAAUCGUGAUCCAGUUGCUCGAGCAGCAACGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGG
..((((...(((.((((..(((((((.((((((((.......))).))))).))))))).(..((((...(....).(((((...)))))......))))..))))).)))...)))).. ( -43.40)
>DroSim_CAF1 391 120 + 1
CGGAUCGCGCAGAUCGUUUAGCAGCUUGGUCAGAUACGGCGAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGG
..((((...(((.((((..(((((((.((((((((.......))).))))).)))))))...(((((.(((....).(((((...)))))....)))))))..)))).)))...)))).. ( -44.60)
>DroEre_CAF1 1601 120 + 1
CGGAUCGCGCAGAUCGUGUAGCAAUUUGGUCAGAUACGGCGAAUCAUGAUCCAGCUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGUGCUGUCCACGAACUGAUAGGUGGG
....((((.(((.(((((.((((.((.((((((((.......))).))))).)).))))...((((((.((....).(((((...)))))...).)))))).))))).)))....)))). ( -39.30)
>DroYak_CAF1 364 120 + 1
CGGAUCGCGCAGGUCGUGUAGCAACUUGGUAAGAUACGGCGAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCGAAGGUACUGUCCACGAACUGAUAGGUGGG
.((((((((...(((((((.((......))...)))))))....)))))))).((((((.....))))))(....).(((((...)))))...........((((..........)))). ( -40.10)
>consensus
CGGAUCGCGCAGAUCGUGUAGCAACUUGGUCAGAUACGGCGAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGG
..((((...(((.(((((.(((((((.((((((((.......))).))))).)))))))...((((((.((....).(((((...)))))...).)))))).))))).)))...)))).. (-36.99 = -38.92 +   1.94)

alignment

secondary structure

dotplot

Window 2

Location	11,190,881 – 11,191,001
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-46.52
Consensus MFE	-38.17
Energy contribution	-39.80
Covariance contribution	1.63
Combinations/Pair	1.06
Mean z-score	-2.02
Structure conservation index	0.82
SVM decision value	0.77
SVM RNA-class probability	0.845670
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11190881 120 + 22224390
GAAUCGUGAUCCAGUUGCUCGAGCAGCAACGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGGCAACUCGCCGGUCACACGUUGCAUCUCGGGCAGCUGGUAG
..........(((((((((((((..((((((......(((((...)))))...(((.(((((........)))))..((((.....)))))))...))))))..)))))))))))))... ( -52.50)
>DroSim_CAF1 431 120 + 1
GAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGGCGCCUCGCCGGUCACACGUCGCAUCUCGGGCAGCUGGUAG
..........((((((((((.((..((.(((......(((((...)))))..((((((((.((...........)).)))))))))))((......))..))..)).))))))))))... ( -47.00)
>DroEre_CAF1 1641 120 + 1
GAAUCAUGAUCCAGCUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGUGCUGUCCACGAACUGAUAGGUGGGCUCCUCACCGGUCACACGUUCCAUUUCGGGCUGCUGGUAG
..........(((((.((.((.((((((.((....).(((((...)))))...).))))))....((((((((.((((((...)))))).))))...))))......)))).)))))... ( -46.00)
>DroYak_CAF1 404 120 + 1
GAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCGAAGGUACUGUCCACGAACUGAUAGGUGGGCUCCUCGCCGGUCACACGUUUCAUCUCCGGCUGCUGGUAG
.....(..((...))..).((((((((..((((....(((((...)))))(((((......))(((...((((.((((((...)))))).))))..))))))...))))))))))))... ( -40.60)
>consensus
GAAUCGUGAUCCAGUUGCUCCAGCAGCAGCGGAAACAGGCUAACAUAGCCAAAGGCGCUGUCCACGAACUGAUAGGUCGGCUCCUCGCCGGUCACACGUUGCAUCUCGGGCAGCUGGUAG
..........((((((((((..((((((.((....).(((((...)))))...).))))))..(((...((((.((((((...)))))).))))..)))........))))))))))... (-38.17 = -39.80 +   1.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:33 2006