Locus 1324

Sequence ID 2L_DroMel_CAF1
Location 3,482,348 – 3,482,477
Length 129
Max. P 0.543965
window2165 window2166

overview

Window 5

Location 3,482,348 – 3,482,449
Length 101
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 71.82
Mean single sequence MFE -36.82
Consensus MFE -16.90
Energy contribution -20.59
Covariance contribution 3.69
Combinations/Pair 1.28
Mean z-score -1.66
Structure conservation index 0.46
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3482348 101 + 22407834
UUUUGCGGUGUACCG-AGCUAAAACUA---ACUGGUUGUGGCCGGCCGGUAAAUCGGUGGAUCGGU-------GAAUCGCUGAGUUGCUGGAUCGAGGUAACCGCUACUGUA
....(((((.((((.-.((((.((((.---...)))).))))((((((((((.(((((((.((...-------)).))))))).))))))).))).)))))))))....... ( -39.40)
>DroVir_CAF1 18514 97 + 1
UUU-GCGGCGCAC----GCUUACAGCAGCCACUG--UG---CGAGCUGUCGAGUCUGUGGACCGGACUCCGACCAAGCUCUCAGCU--UAACUCG---AGCUGUGGCCCGUA
..(-((((.....----((.....)).(((((..--.(---.(((((((((((((((.....)))))).))))..))))).)((((--(.....)---)))))))))))))) ( -38.80)
>DroSim_CAF1 9567 101 + 1
UUUUGCGGUGUGCCG-AGCUAAAACUA---ACUGGUUGUGGCCGGCCGGUAGAUCGGUGGAUCGGU-------GAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUA
....(((((.((((.-.((((.((((.---...)))).))))((((((((((...(((((.((...-------)).)))))...))))))).))).)))))))))....... ( -34.70)
>DroEre_CAF1 9855 101 + 1
UUUUGCGGUGUGCCG-AGCUAAAACCA---ACUGGUUGUGGCCGGCCGGUAGAUCGGCGGAUCGGU-------GAAUCGCUAAGCUGCUGGAUCGAGGUAACCGCUACUGUA
....(((((.((((.-.((((.((((.---...)))).))))((((((((((...(((((.((...-------)).)))))...))))))).))).)))))))))....... ( -41.30)
>DroYak_CAF1 9620 94 + 1
CUUUGCGGUGAGCCGUAGCUUAAACUA---ACUGGUUGUGGCCGGCCGGUAGAU--------CGGU-------GAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUA
....(((((..(((...(((..((((.---...))))..)))((((((((((..--------.(((-------(...))))...))))))).))).))).)))))....... ( -29.90)
>consensus
UUUUGCGGUGUGCCG_AGCUAAAACUA___ACUGGUUGUGGCCGGCCGGUAGAUCGGUGGAUCGGU_______GAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUA
....(((((.((((...((((.(((((.....))))).))))((((((((((...((((..................))))...))))))).))).)))))))))....... (-16.90 = -20.59 +   3.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,482,380 – 3,482,477
Length 97
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 73.39
Mean single sequence MFE -32.07
Consensus MFE -12.62
Energy contribution -13.51
Covariance contribution 0.89
Combinations/Pair 1.17
Mean z-score -1.90
Structure conservation index 0.39
SVM decision value 0.02
SVM RNA-class probability 0.543965
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3482380 97 + 22407834
UGUGGCCGGCCGGUAAAUCGGUG--GAUCGGUGAAUCGCUGAGUUGCUGGAUCGAGGUAACCGCUACUGUAAUUGGCGUGAUAUUUCAUGCGGAGAUCA
.(((((((((((((((.((((((--(.((...)).))))))).))))))).))).((...))))))).(...((.((((((....)))))).))...). ( -35.00)
>DroPse_CAF1 11183 84 + 1
UGCUGCUUGUCGGCUUACUGUUGCUUACUGGUGGAUCGCUG--------G-------AGCUCGCUCCAGUAAUUGGCGUGAUAUUUCAUGCAUCGAUCA
....(((.((.(((........))).)).))).((((((((--------(-------((....))))))).....((((((....))))))...)))). ( -31.00)
>DroSim_CAF1 9599 97 + 1
UGUGGCCGGCCGGUAGAUCGGUG--GAUCGGUGAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUAAUUGGCGUGAUAUUUCAUGCGGAGAUCA
.(((((((((((((((...((((--(.((...)).)))))...))))))).))).((...))))))).(...((.((((((....)))))).))...). ( -30.30)
>DroEre_CAF1 9887 97 + 1
UGUGGCCGGCCGGUAGAUCGGCG--GAUCGGUGAAUCGCUAAGCUGCUGGAUCGAGGUAACCGCUACUGUAAUUGGCGUGAUUUUUCAUGCGGAGAUCA
.(((((((((((((((...((((--(.((...)).)))))...))))))).))).((...))))))).(...((.((((((....)))))).))...). ( -34.40)
>DroYak_CAF1 9653 89 + 1
UGUGGCCGGCCGGUAGAU----------CGGUGAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUAAUUGGCGUGAUUUUUCAUGCGGAGAUCA
.(((((((((((((((..----------.((((...))))...))))))).))).((...))))))).(...((.((((((....)))))).))...). ( -28.10)
>DroPer_CAF1 11259 84 + 1
UGCCGCUUGUCGGCUUACUGUUGCUUACUGGUGGAUCGCUG--------G-------AGCUCGCUCCAGUAAUUGGCGUGAUAUUUCAUGCAUCGAUCA
...((((.((.(((........))).)).))))((((((((--------(-------((....))))))).....((((((....))))))...)))). ( -33.60)
>consensus
UGUGGCCGGCCGGUAGAUCGGUG__GAUCGGUGAAUCGCUAAGUUGCUGGAUCGAGGUAACCGCUACUGUAAUUGGCGUGAUAUUUCAUGCGGAGAUCA
.(((((..(((((..............))))).....((......))...............)))))........((((((....))))))........ (-12.62 = -13.51 +   0.89)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:41 2006