Locus 5068

Sequence ID 2L_DroMel_CAF1
Location 14,499,473 – 14,499,602
Length 129
Max. P 0.994362
window8064 window8065 window8066

overview

Window 4

Location 14,499,473 – 14,499,576
Length 103
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 96.00
Mean single sequence MFE -23.41
Consensus MFE -21.50
Energy contribution -21.54
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.92
SVM decision value 2.47
SVM RNA-class probability 0.994362
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14499473 103 + 22407834
-----GCCGCUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
-----(((((((.....((((...........))))...)))))))..(((((...........))))).....(((((............)))))............ ( -23.80)
>DroSec_CAF1 31178 103 + 1
-----GCCGCUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
-----(((((((.....((((...........))))...)))))))..(((((...........))))).....(((((............)))))............ ( -23.80)
>DroSim_CAF1 15212 103 + 1
-----GCCGCUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
-----(((((((.....((((...........))))...)))))))..(((((...........))))).....(((((............)))))............ ( -23.80)
>DroYak_CAF1 20434 108 + 1
CUCUUGCUGCUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
.((.((.((((((((..((((...........)))).....((((((((((((...........))))).....)))))))...........).))))))))).)).. ( -26.30)
>DroPer_CAF1 17943 103 + 1
-----UGUGUUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAACGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
-----(((((((((.((((....)))).....(((.......(((((((((((...........))))).....))))))...........))))))))))))..... ( -19.37)
>consensus
_____GCCGCUGUCCGAUGGCCACAUUAUUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUU
........(((((((..((((...........)))).....((((((((((((...........))))).....)))))))...........).))))))........ (-21.50 = -21.54 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,499,496 – 14,499,602
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.13
Mean single sequence MFE -27.13
Consensus MFE -19.28
Energy contribution -19.76
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.71
SVM decision value 0.65
SVM RNA-class probability 0.812436
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14499496 106 + 22407834
UUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGGAGUGGCUGCUG------------C--UGGG
..........(((((((((((...(((((.......)))))...((((.(((....((((((...((........)).))))))...))))))))))))))------------)--))). ( -27.80)
>DroSec_CAF1 31201 112 + 1
UUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGGAGUGGCUGCUG------CUGCUGC--CGGG
.....((....((((((((((((.(((((.......)))))...((((.(((....((((((...((........)).))))))...))))))).))))))------)))))).--..)) ( -31.50)
>DroEre_CAF1 25171 108 + 1
UUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGGAGUGGCUGCUGCUG------------CUGU
...........((((((((((((.(((((.......)))))...((((.(((....((((((...((........)).))))))...))))))).)))))))))------------))). ( -30.30)
>DroYak_CAF1 20462 120 + 1
UUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGGAGUGGCUGCUGCUGCUUCUGCUUCUGCUGG
...........((((((.((((((..(((((((.....(((.....(((((............))))))))......)))))))......((..((....))..)))))))).)))))). ( -32.60)
>DroPer_CAF1 17966 96 + 1
UUAAGCCAAUUCAACGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGAAGCUGU------------------------
....(((........))).((((.......((((((.(.((.....(((((............))))).....)).).))))))........))))------------------------ ( -13.46)
>consensus
UUAAGCCAAUUCAGCGGCAGCAGAUAAAUAAAUAAAAUUUGAAACAUUGCCGCAACAAUAAAAGGCGACAGUACACGAUUUAUUAAACGGAGUGGCUGCUG____________C__CGGG
...(((((.(((.((((((((((((...........))))).....)))))))...((((((...((........)).))))))....))).)))))....................... (-19.28 = -19.76 +   0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,499,496 – 14,499,602
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.13
Mean single sequence MFE -26.34
Consensus MFE -18.10
Energy contribution -18.38
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 0.01
SVM RNA-class probability 0.537824
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14499496 106 - 22407834
CCCA--G------------CAGCAGCCACUCCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGCUGAAUUGGCUUAA
..((--(------------(.(((((....((((.(((((((..(((......)))..)))))))..)))).........((((.......))))....))))).))))........... ( -25.10)
>DroSec_CAF1 31201 112 - 1
CCCG--GCAGCAG------CAGCAGCCACUCCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGCUGAAUUGGCUUAA
.(((--.((((.(------((((((.....((((.(((((((..(((......)))..)))))))..)))).........((((.......))))..))))))).))))...)))..... ( -30.70)
>DroEre_CAF1 25171 108 - 1
ACAG------------CAGCAGCAGCCACUCCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGCUGAAUUGGCUUAA
.(((------------(.(((((((.....((((.(((((((..(((......)))..)))))))..)))).........((((.......))))..))))))).))))........... ( -29.20)
>DroYak_CAF1 20462 120 - 1
CCAGCAGAAGCAGAAGCAGCAGCAGCCACUCCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGCUGAAUUGGCUUAA
.......((((.....((((.(((((....((((.(((((((..(((......)))..)))))))..)))).........((((.......))))....))))).)))).....)))).. ( -30.40)
>DroPer_CAF1 17966 96 - 1
------------------------ACAGCUUCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGUUGAAUUGGCUUAA
------------------------..(((.......((((((...((.((((((((...........))))))..))..))...)))))).........)))((((......)))).... ( -16.29)
>consensus
CCAG__G____________CAGCAGCCACUCCGUUUAAUAAAUCGUGUACUGUCGCCUUUUAUUGUUGCGGCAAUGUUUCAAAUUUUAUUUAUUUAUCUGCUGCCGCUGAAUUGGCUUAA
.......................(((((.......(((((((..(((......)))..)))))))..((((((..((...((((.......))))....)))))))).....)))))... (-18.10 = -18.38 +   0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:08 2006