Locus 5803

Sequence ID X_DroMel_CAF1
Location 15,047,546 – 15,047,732
Length 186
Max. P 0.937826
window9414 window9415 window9416

overview

Window 4

Location 15,047,546 – 15,047,662
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.73
Mean single sequence MFE -36.58
Consensus MFE -28.20
Energy contribution -27.92
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.77
SVM decision value 0.54
SVM RNA-class probability 0.775133
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15047546 116 + 22224390
GGGGG-CUUUGGGC-CAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGCCUCCAAAUUGGCUGAGGGAAGAAAGUUUUCCUUGCGGCUACUUUCGCCGC--UGCUCGGUCACCGAUGUCG
(((((-(..(((((-..............))))).(((......)))))))))....((((((((((((((...))))))..(((((.......)))))--..))))))))......... ( -37.94)
>DroSec_CAF1 3458 115 + 1
-GGGG-CUUUGGGC-CAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGGCUCCAAAUUGGCUGAGGGAAGAAAGUUUUCCUUGCGGCUACUUUCGCCGC--UGCUCGGUCACCGAUGUCG
-((((-(..(((((-..............)))))((((......)))))))))....((((((((((((((...))))))..(((((.......)))))--..))))))))......... ( -38.04)
>DroAna_CAF1 2997 109 + 1
---------CGGGCUGAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGGCCCCAAAUUGGCUGAGGGAGGAAAGUUUUCCUUGCGGCUACUUUCGCCGCCCUGCUCGGCGACACAUCC--
---------(((((.(((((((((((...(....)......(((((..(((.......)))..))))))))))))))))...(((((.......)))))...)))))...........-- ( -37.10)
>DroEre_CAF1 3232 111 + 1
------CUUUGGGC-CAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGGCUCCAAAUUGGCUGAGGGAAGAAAGUUUUGCUUGCGGCUACUUUCGCCGC--UGCUCGGUCACCGAUGUCG
------.....(((-(((((((((((...(....)......(((((..(((.......)))..)))))))))))))))((..(((((.......)))))--.))..)))).......... ( -34.10)
>DroYak_CAF1 3815 117 + 1
GGGGGCUUUUGGGC-CAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGGCUCCAAAUUGGCUGAGGGAAGAAAGUUUUACUUGCGGCUACUUUCGCCGC--UGCUCGGUCACCGAUGUCG
((.((((...((((-.((((((((((...(....)......(((((..(((.......)))..)))))))))))))))....(((((.......)))))--.)))))))).))....... ( -35.70)
>consensus
_GGGG_CUUUGGGC_CAAAACUUUCUAUAGCCUACAAAUUUUCUUUUGGCUCCAAAUUGGCUGAGGGAAGAAAGUUUUCCUUGCGGCUACUUUCGCCGC__UGCUCGGUCACCGAUGUCG
.........(((((..((((((((((...(....)......((((((((((.......))))))))))))))))))))....(((((.......)))))...)))))............. (-28.20 = -27.92 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,047,624 – 15,047,732
Length 108
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 89.21
Mean single sequence MFE -25.25
Consensus MFE -20.62
Energy contribution -20.88
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.82
SVM decision value 0.37
SVM RNA-class probability 0.706787
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15047624 108 + 22224390
UUGCGGCUACUUUCGCCGCUGCUCGGUCACCGAUGUCGCAGCACGAUGGCCUAGUCCAUCUAUAUCCACAUCUUUAUCUCCU-UUGCCAGCUCCAUUCAUCUCGACCCA
..(((((.......))))).....((((...((((..(.(((..(((((......)))))........((............-.))...))).)...))))..)))).. ( -24.42)
>DroSec_CAF1 3535 108 + 1
UUGCGGCUACUUUCGCCGCUGCUCGGUCACCGAUGUCGCAGGACGAUGGCCUAGUCCAUCUAUAUCCACAUCUUUAUCUCCU-UUGCCAGCUCCAUUCAUCUCGCCCCA
..(((((.......))))).(((.(((.......(((....)))(((((......)))))......................-..)))))).................. ( -23.00)
>DroEre_CAF1 3305 106 + 1
UUGCGGCUACUUUCGCCGCUGCUCGGUCACCGAUGUCGCAGCCAGAUGGCCAAGUCCAUCUAUAUCCACAUCUUUAUCUGCU-UGGCAAGCACCAUGCCUCCCCUCC--
..(((((.......)))(((((((((...))))....))))).((((((......))))))..................)).-.((((.......))))........-- ( -26.90)
>DroYak_CAF1 3894 107 + 1
UUGCGGCUACUUUCGCCGCUGCUCGGUCACCGAUGUCGCAGCAAGAUGGCCUAGUCCAUCUAUAUCCACAUCUUUAUCUCCUCUAGCCAGCUUCGUUCCCCUCUUUC--
..(((((((........(((((((((...))))....))))).((((((......))))))......................))))).))................-- ( -26.70)
>consensus
UUGCGGCUACUUUCGCCGCUGCUCGGUCACCGAUGUCGCAGCAAGAUGGCCUAGUCCAUCUAUAUCCACAUCUUUAUCUCCU_UUGCCAGCUCCAUUCAUCUCGUCC__
..(((((.......)))(((((((((...))))....)))))..(((((......))))).............................)).................. (-20.62 = -20.88 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,047,624 – 15,047,732
Length 108
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 89.21
Mean single sequence MFE -34.88
Consensus MFE -29.58
Energy contribution -29.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.85
SVM decision value 1.26
SVM RNA-class probability 0.937826
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15047624 108 - 22224390
UGGGUCGAGAUGAAUGGAGCUGGCAA-AGGAGAUAAAGAUGUGGAUAUAGAUGGACUAGGCCAUCGUGCUGCGACAUCGGUGACCGAGCAGCGGCGAAAGUAGCCGCAA
..(((((...(((.((..((.((((.-.....(((....))).......(((((......))))).))))))..))))).))))).....(((((.......))))).. ( -33.60)
>DroSec_CAF1 3535 108 - 1
UGGGGCGAGAUGAAUGGAGCUGGCAA-AGGAGAUAAAGAUGUGGAUAUAGAUGGACUAGGCCAUCGUCCUGCGACAUCGGUGACCGAGCAGCGGCGAAAGUAGCCGCAA
((.(((............((((.(..-.((..((...(((((.(.....(((((......)))))......).))))).))..))..))))).((....)).))).)). ( -33.40)
>DroEre_CAF1 3305 106 - 1
--GGAGGGGAGGCAUGGUGCUUGCCA-AGCAGAUAAAGAUGUGGAUAUAGAUGGACUUGGCCAUCUGGCUGCGACAUCGGUGACCGAGCAGCGGCGAAAGUAGCCGCAA
--....((.((((.....)))).)).-.((.......(((((.(...(((((((......)))))))....).)))))(....)...)).(((((.......))))).. ( -39.90)
>DroYak_CAF1 3894 107 - 1
--GAAAGAGGGGAACGAAGCUGGCUAGAGGAGAUAAAGAUGUGGAUAUAGAUGGACUAGGCCAUCUUGCUGCGACAUCGGUGACCGAGCAGCGGCGAAAGUAGCCGCAA
--....................(((...((..((...(((((.(....((((((......)))))).....).))))).))..)).))).(((((.......))))).. ( -32.60)
>consensus
__GGACGAGAGGAAUGGAGCUGGCAA_AGGAGAUAAAGAUGUGGAUAUAGAUGGACUAGGCCAUCGUGCUGCGACAUCGGUGACCGAGCAGCGGCGAAAGUAGCCGCAA
..................(((.(..............(((((.(.....(((((......)))))......).)))))(....)).))).(((((.......))))).. (-29.58 = -29.57 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:44 2006