Locus 5368

Sequence ID 2L_DroMel_CAF1
Location 15,234,654 – 15,234,796
Length 142
Max. P 0.947005
window8521 window8522 window8523

overview

Window 1

Location 15,234,654 – 15,234,760
Length 106
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.34
Mean single sequence MFE -25.60
Consensus MFE -16.95
Energy contribution -17.32
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.24
Structure conservation index 0.66
SVM decision value 0.11
SVM RNA-class probability 0.586315
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15234654 106 + 22407834
-------UUGGUUUUACCU-AGCUUUUGCAUUUC-GU-UU--UCUGCGUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUCGGCAACGGCAGCC
-------..((.....)).-.((....)).....-..-..--.((((..(((((((((((....))))))........(..(((((((.......)))))))..))))))..)))).. ( -23.60)
>DroVir_CAF1 249414 101 + 1
-------UUGGCGUUC-------GUUUGUGUUCA-GCGUU--UCUGCGUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUUGGCAGCGGCAAUG
-------(((.(((..-------..........(-((((.--...)))))((((((((((....))))))...........(((((((.......)))))))...))))))).))).. ( -22.20)
>DroPse_CAF1 253972 102 + 1
-------UUAGUUUUGGGU-UCGUUUUGAGUUUC-GU-UU--UCUGCGUUUGCCGCUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUCGGCAACGGC----
-------............-((((((((((((..-..-..--...((((((((.((.......))))))))))..........(((((.......)))))))))))).))))).---- ( -20.70)
>DroGri_CAF1 221444 91 + 1
-------U-----------------UUGUGUUCA-GCAUU--GCUGCAUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUUGGCAACGGCAAUG
-------.-----------------.........-.((((--((((...(((((((((((....))))))...........(((((((.......)))))))...))))))))))))) ( -23.70)
>DroWil_CAF1 274323 117 + 1
CUUAUGUUUAGUUUUAGUUUUCAUUUUGCGUUGCCGU-UGCCUGUGCGUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUCGGCAAUGGCAACG
............................(((((((((-((((((..((.((((....)))).))..))..........(..(((((((.......)))))))..)))))))))))))) ( -36.80)
>DroMoj_CAF1 276136 101 + 1
-------UUGGCGUUC-------GUUUGUGCUCA-GCGCU--GCUGCGUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUUGGCAACGGCAAUG
-------(((.(((((-------(((((..(...-((((.--...))))((((....))))..)..)))))).(((..((..((((((.......))))))))..))))))).))).. ( -26.60)
>consensus
_______UUGGUUUUA_______UUUUGUGUUCA_GC_UU__UCUGCGUUUGCCUUUGCAAUUGUGCAAAUGUGUUUUGUUUUGAUAAAUUAGGCUUGUCAACUCGGCAACGGCAAUG
............................................(((..(((((((((((....))))))...........(((((((.......)))))))...)))))..)))... (-16.95 = -17.32 +   0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,234,654 – 15,234,760
Length 106
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.34
Mean single sequence MFE -19.33
Consensus MFE -14.54
Energy contribution -14.90
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -1.96
Structure conservation index 0.75
SVM decision value 1.37
SVM RNA-class probability 0.947005
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15234654 106 - 22407834
GGCUGCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA--AA-AC-GAAAUGCAAAAGCU-AGGUAAAACCAA-------
..((((..((((((..((((.(((.....))).))))..)........((((((....)))))))))))..)))).--..-..-.....((....)).-.((.....))..------- ( -21.30)
>DroVir_CAF1 249414 101 - 1
CAUUGCCGCUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA--AACGC-UGAACACAAAC-------GAACGCCAA-------
..((((...((((...((((.(((.....))).))))...........((((((....))))))))))...)))).--.....-...........-------.........------- ( -14.90)
>DroPse_CAF1 253972 102 - 1
----GCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAGCGGCAAACGCAGA--AA-AC-GAAACUCAAAACGA-ACCCAAAACUAA-------
----..((((...(((((................................((((....))))(((.....)))...--..-..-..)))))..)))).-............------- ( -15.70)
>DroGri_CAF1 221444 91 - 1
CAUUGCCGUUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAAUGCAGC--AAUGC-UGAACACAA-----------------A-------
((((((.((((((...((((.(((.....))).))))...........((((((....))))))))))...)).))--)))).-.........-----------------.------- ( -18.80)
>DroWil_CAF1 274323 117 - 1
CGUUGCCAUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCACAGGCA-ACGGCAACGCAAAAUGAAAACUAAAACUAAACAUAAG
(((((((.(((((..(((.....((((..(((........)))......(((((....))))))))).))).....))))-).)))))))............................ ( -26.70)
>DroMoj_CAF1 276136 101 - 1
CAUUGCCGUUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGC--AGCGC-UGAGCACAAAC-------GAACGCCAA-------
...((((((((((...((((.(((.....))).))))...........((((((....))))))))).))))((((--...))-)).))).....-------.........------- ( -18.60)
>consensus
CAUUGCCGUUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA__AA_AC_GGAACACAAAA_______GAAAACCAA_______
..((((..(((((((((((.......))))))................((((((....)))))))))))..))))........................................... (-14.54 = -14.90 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,234,684 – 15,234,796
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.76
Mean single sequence MFE -23.75
Consensus MFE -15.03
Energy contribution -15.33
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -1.87
Structure conservation index 0.63
SVM decision value 1.32
SVM RNA-class probability 0.941656
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15234684 112 - 22407834
CUCCUUCGCCCACCGCACCACCCAUUUUGGCGCU----CUG--GCUGCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA
.........(((..((.(((.......))).)).----.))--)((((..((((((..((((.(((.....))).))))..)........((((((....)))))))))))..)))). ( -27.10)
>DroVir_CAF1 249439 84 - 1
----------------------------CUCGCU----CCC--AUUGCCGCUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA
----------------------------......----...--.((((...((((...((((.(((.....))).))))...........((((((....))))))))))...)))). ( -14.90)
>DroPse_CAF1 254002 101 - 1
CCUCUUC-----AUGCCCCACCCAUUGUGGCGCC------------GCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAGCGGCAAACGCAGA
..(((.(-----..((.((((.....)))).)).------------((((((((.((((((.......)))))).......((((.....)))).......))))))))....).))) ( -22.60)
>DroEre_CAF1 184157 111 - 1
-CUCUGCGCCCACCGCACCACCCAUUUUGGCGCU----UGG--GCUGCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA
-.((((((((((..((.(((.......))).)).----)))--))(((((((......((((.(((.....))).)))).....)))...((((((....))))))))))...))))) ( -34.70)
>DroMoj_CAF1 276161 85 - 1
---------------------------UCUCGUU----UCC--AUUGCCGUUGCCAAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGC
---------------------------.......----...--.((((..(((((...((((.(((.....))).))))...........((((((....)))))))))))..)))). ( -16.20)
>DroAna_CAF1 190841 108 - 1
CUUCUU----------UCCACCCAUUUUGGCGCUAGCUCCGGCGCUGGCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA
......----------............((((((......)))))).(((((((((..((((.(((.....))).))))..)........((((((....))))))))).)))))... ( -27.00)
>consensus
__UCUU___________CCACCCAUUUUGGCGCU____CCG__GCUGCCGUUGCCGAGUUGACAAGCCUAAUUUAUCAAAACAAAACACAUUUGCACAAUUGCAAAGGCAAACGCAGA
............................................((((..(((((((((((.......))))))................((((((....)))))))))))..)))). (-15.03 = -15.33 +   0.31)

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 11:42:25 2006