Locus 5484

Sequence ID 2L_DroMel_CAF1
Location 15,659,562 – 15,659,652
Length 90
Max. P 0.987859
window8702 window8703

overview

Window 2

Location 15,659,562 – 15,659,652
Length 90
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 70.22
Mean single sequence MFE -23.82
Consensus MFE -19.51
Energy contribution -18.96
Covariance contribution -0.55
Combinations/Pair 1.28
Mean z-score -1.73
Structure conservation index 0.82
SVM decision value 2.10
SVM RNA-class probability 0.987859
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15659562 90 + 22407834
AUUCACGCAGGAGGAUAAUACCAUCCUUGCGCUUCACUUCGAUGUCGUUGUCCUUGAAGCGCUGCAAAUGAAAAAACGAAA------------UCAUCAGA---------U--
.((((.(((.((((((......))))))((((((((....(((......)))..)))))))))))...)))).........------------........---------.-- ( -22.90)
>DroVir_CAF1 37210 81 + 1
AUUCACGCAGCAGGAUAAUGCCAUCCUUGCGCUUCACUUCGAUGUCAUUGUCCUUAAAGCGCUGCAAAA---CA----AAAGAGAA-------------------------AU
......((((((((((((((.((((...............)))).)))))))))......)))))....---..----........-------------------------.. ( -21.56)
>DroPse_CAF1 18302 111 + 1
GUUCACGCAGUAGGAUAAUGCCGUCCUUGCGCUUCACCUCGAUGUCGUUGUCCUUGAAGCGCUGCAAAUGGACAAGCGGAAAAGCAAAUAUAAUUUCCAAAUACGAUGCGU--
....(((((((.((......))((((..((((((((....(((......)))..)))))))).......))))..))(((((...........)))))........)))))-- ( -29.00)
>DroGri_CAF1 20613 73 + 1
AUUCACGCAGCAGGAUAAUGCCAUCCUUGCGCUUCACCUCGAUGUCAUUGUCCUUAAAGCGCUGUAAAAA---A----CA---------------------------------
......((((((((((((((.((((...............)))).)))))))))......))))).....---.----..--------------------------------- ( -19.16)
>DroWil_CAF1 37846 99 + 1
AUUCACGUAGCAGGAUAAUGCCAUCCUUACGCUUCACUUCGAUGUCGUUGUCCUUGAAGCGCUGCAA-UGAAAAAGACGAAAACCAA---CAAAUCACAAAUA----------
.((((.((((((((((......)))))...((((((....(((......)))..)))))))))))..-))))...............---.............---------- ( -21.30)
>DroPer_CAF1 16013 111 + 1
GUUCACGCAGUAGGAUAAUGCCGUCCUUGCGCUUCACCUCGAUGUCGUUGUCCUUGAAGCGCUGCAAAUGGACAAGCGGAAAAGCAAAUAUAAUUUCCAAAUACGAUGCGU--
....(((((((.((......))((((..((((((((....(((......)))..)))))))).......))))..))(((((...........)))))........)))))-- ( -29.00)
>consensus
AUUCACGCAGCAGGAUAAUGCCAUCCUUGCGCUUCACCUCGAUGUCGUUGUCCUUGAAGCGCUGCAAAUG_ACAAGCGGAAAAGCA_______UU__CAAA____________
......((((((((((((((.((((...............)))).)))))))))......)))))................................................ (-19.51 = -18.96 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,659,562 – 15,659,652
Length 90
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 70.22
Mean single sequence MFE -23.90
Consensus MFE -17.94
Energy contribution -17.72
Covariance contribution -0.22
Combinations/Pair 1.19
Mean z-score -0.63
Structure conservation index 0.75
SVM decision value 0.24
SVM RNA-class probability 0.646785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15659562 90 - 22407834
--A---------UCUGAUGA------------UUUCGUUUUUUCAUUUGCAGCGCUUCAAGGACAACGACAUCGAAGUGAAGCGCAAGGAUGGUAUUAUCCUCCUGCGUGAAU
--.---------...((((.------------...))))..(((((..((.((((((((.......((....))...)))))))).((((.((......))))))))))))). ( -24.10)
>DroVir_CAF1 37210 81 - 1
AU-------------------------UUCUCUUU----UG---UUUUGCAGCGCUUUAAGGACAAUGACAUCGAAGUGAAGCGCAAGGAUGGCAUUAUCCUGCUGCGUGAAU
..-------------------------........----..---....(((((((((((..((........))....))))))...((((((....)))))))))))...... ( -19.60)
>DroPse_CAF1 18302 111 - 1
--ACGCAUCGUAUUUGGAAAUUAUAUUUGCUUUUCCGCUUGUCCAUUUGCAGCGCUUCAAGGACAACGACAUCGAGGUGAAGCGCAAGGACGGCAUUAUCCUACUGCGUGAAC
--(((((..(((...(((((...........)))))(((.((((.((....(((((((....((..((....))..)))))))))))))))))).......)))))))).... ( -29.50)
>DroGri_CAF1 20613 73 - 1
---------------------------------UG----U---UUUUUACAGCGCUUUAAGGACAAUGACAUCGAGGUGAAGCGCAAGGAUGGCAUUAUCCUGCUGCGUGAAU
---------------------------------..----.---........((((....((((.((((.((((...(((...)))...)))).)))).))))...)))).... ( -19.90)
>DroWil_CAF1 37846 99 - 1
----------UAUUUGUGAUUUG---UUGGUUUUCGUCUUUUUCA-UUGCAGCGCUUCAAGGACAACGACAUCGAAGUGAAGCGUAAGGAUGGCAUUAUCCUGCUACGUGAAU
----------.............---...............((((-(.((.((((((((.......((....))...)))))))).((((((....))))))))...))))). ( -20.80)
>DroPer_CAF1 16013 111 - 1
--ACGCAUCGUAUUUGGAAAUUAUAUUUGCUUUUCCGCUUGUCCAUUUGCAGCGCUUCAAGGACAACGACAUCGAGGUGAAGCGCAAGGACGGCAUUAUCCUACUGCGUGAAC
--(((((..(((...(((((...........)))))(((.((((.((....(((((((....((..((....))..)))))))))))))))))).......)))))))).... ( -29.50)
>consensus
____________UUUG__AA_______UGCUUUUCCGCUUGU_CAUUUGCAGCGCUUCAAGGACAACGACAUCGAAGUGAAGCGCAAGGAUGGCAUUAUCCUGCUGCGUGAAU
.............................................(((((.((((((((.......((....))...)))))))).((((((....)))))).....))))). (-17.94 = -17.72 +  -0.22)

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 11:45:16 2006