Locus 4745

Sequence ID 2R_DroMel_CAF1
Location 15,582,485 – 15,582,624
Length 139
Max. P 0.963362
window7634 window7635 window7636 window7637

overview

Window 4

Location 15,582,485 – 15,582,588
Length 103
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.79
Mean single sequence MFE -36.22
Consensus MFE -21.32
Energy contribution -21.85
Covariance contribution 0.53
Combinations/Pair 1.10
Mean z-score -2.14
Structure conservation index 0.59
SVM decision value 1.55
SVM RNA-class probability 0.963362
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15582485 103 + 20766785
GGAGCAAGUGGAUCGGAGGAUCCGUAAGAUCGGUGGAUCGGUGGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU-UCGGCAUUUCU
((((((((((((((....)))))....((((....))))....)))))..(((((((.((((((((.........)))))))))))))))))-))......... ( -37.70)
>DroVir_CAF1 522114 85 + 1
UGUGCAAGUUGCUCGACGGCU-------------------GCCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCUUUCGGCAUUUCU
...((..(((....))).))(-------------------((((...((.(((((((.((((((((.........))))))))))))))).)).)))))..... ( -30.00)
>DroSim_CAF1 355900 103 + 1
GGAGCAAGUGGAUCGGAGGAUCCGUAAGAUCGGUGGAUCGGUGGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU-UCGGCAUUUCU
((((((((((((((....)))))....((((....))))....)))))..(((((((.((((((((.........)))))))))))))))))-))......... ( -37.70)
>DroWil_CAF1 698947 91 + 1
AG--------GCCCGGAGGCAACUGCAACUCGG-----CAGUCGUUUGACAACUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCUUUCGGCAUUUCU
..--------(((.(((((.((.(((......(-----((((.(.....).))))).(((((((((.........)))))))))))).))))))))))...... ( -33.10)
>DroAna_CAF1 350666 98 + 1
GGAGCAAGUGGUUCGGUGGCUCGCUGAGG---CUGCCCCGCUUG--UGACAAACGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU-UCGGCAUUUCU
(..((((((((...((..(((......))---)..)))))))))--)..)....(((.((((((((.........)))))))))))......-........... ( -38.90)
>DroPer_CAF1 383734 102 + 1
GGAGCAAGUUGCUCGACGGCUGCUG-CUGCUGCUCCCGCUGCCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCC-UCGGCAUUUCU
(((((((((((.....)))))((..-..))))))))...(((((...((..((((((.((((((((.........)))))))))))))))).-.)))))..... ( -39.90)
>consensus
GGAGCAAGUGGCUCGGAGGCUCCGU_AGAUCGGUG___CGGUCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU_UCGGCAUUUCU
........................................((((...((..((((((.((((((((.........))))))))))))))))...))))...... (-21.32 = -21.85 +   0.53)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,582,485 – 15,582,588
Length 103
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.79
Mean single sequence MFE -30.92
Consensus MFE -17.41
Energy contribution -17.43
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -1.60
Structure conservation index 0.56
SVM decision value 0.26
SVM RNA-class probability 0.655714
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15582485 103 - 20766785
AGAAAUGCCGA-AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCCACCGAUCCACCGAUCUUACGGAUCCUCCGAUCCACUUGCUCC
.........((-..(((((((((.(((((.........))))).)).))))))).)).(((....((((....))))....(((((....)))))....))).. ( -29.60)
>DroVir_CAF1 522114 85 - 1
AGAAAUGCCGAAAGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGGC-------------------AGCCGUCGAGCAACUUGCACA
.((..(((((..(.(((((((((.(((((.........))))).)).))))))).)....))))-------------------)....))..((.....))... ( -29.30)
>DroSim_CAF1 355900 103 - 1
AGAAAUGCCGA-AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCCACCGAUCCACCGAUCUUACGGAUCCUCCGAUCCACUUGCUCC
.........((-..(((((((((.(((((.........))))).)).))))))).)).(((....((((....))))....(((((....)))))....))).. ( -29.60)
>DroWil_CAF1 698947 91 - 1
AGAAAUGCCGAAAGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAGUUGUCAAACGACUG-----CCGAGUUGCAGUUGCCUCCGGGC--------CU
......(((....((..((((((.(((((.........))))).)).))))....))...((((((-----(......)))))))......)))--------.. ( -29.30)
>DroAna_CAF1 350666 98 - 1
AGAAAUGCCGA-AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCGUUUGUCA--CAAGCGGGGCAG---CCUCAGCGAGCCACCGAACCACUUGCUCC
......((.((-..(((((((((.(((((.........))))).)).))))))).)).--....((((((.(---(....))..))).)))........))... ( -30.20)
>DroPer_CAF1 383734 102 - 1
AGAAAUGCCGA-GGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGGCAGCGGGAGCAGCAG-CAGCAGCCGUCGAGCAACUUGCUCC
.(...(((((.-.((((((((((.(((((.........))))).)).))))))..))...))))).).((((((((..-..)).((......))....)))))) ( -37.50)
>consensus
AGAAAUGCCGA_AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGACCG___CACCGACCU_AAGGAGCCUCCGAGCCACUUGCUCC
.........((...(((((((((.(((((.........))))).)).))))))).))............................................... (-17.41 = -17.43 +   0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,582,518 – 15,582,624
Length 106
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.84
Mean single sequence MFE -27.48
Consensus MFE -21.93
Energy contribution -22.40
Covariance contribution 0.47
Combinations/Pair 1.10
Mean z-score -2.29
Structure conservation index 0.80
SVM decision value 1.53
SVM RNA-class probability 0.961428
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15582518 106 + 20766785
UGGAUCGGUGGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU-UCGGCAUUUCUU-UAAAAAUAAAUUUAUGUGGCCGCCUUCGCU-UUGCU--
..((..((((((((((.(((((((.((((((((.........)))))))))))))))..-)))((((...((-((....))))...))))))))))).))...-.....-- ( -34.50)
>DroVir_CAF1 522135 83 + 1
-------GCCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCUUUCGGCAUUUCUU-UAAAAAUAAAUUUAUGUG--------------------
-------((((...((.(((((((.((((((((.........))))))))))))))).)).)))).......-..................-------------------- ( -27.40)
>DroWil_CAF1 698972 96 + 1
-----CAGUCGUUUGACAACUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCUUUCGGCAUUUCUU-UAAAAAUAAAUUUAUGUGGCCGCCUUUGU---------
-----..(((....)))...((((.((((((((.........)))))))))))).......((((.......-((((......))))....)))).......--------- ( -23.60)
>DroMoj_CAF1 585058 84 + 1
-------GCCGCUUGACAAAUGCAACCGCCAACAAAGACGCAGUUGGUGGUGCAUUUCUUUGGGCAUUUCUUUUAAAAAUAAAUUUAUGUG--------------------
-------...(((..(.(((((((.((((((((.........)))))))))))))))..)..)))..........................-------------------- ( -26.40)
>DroAna_CAF1 350696 107 + 1
UGCCCCGCUUG--UGACAAACGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU-UCGGCAUUUCUU-UAAAAAUAAAUUUAUGUGCCCGCCGCCGCCUUCGCUGG
...((.((..(--((.(....(((.((((((((.........)))))))))))......-..(((((.....-((((......)))).)))))....).)))....)).)) ( -26.50)
>DroPer_CAF1 383766 89 + 1
UCCCGCUGCCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCC-UCGGCAUUUCUU-UAAAAAUAAAUUUAUGUG--------------------
......(((((...((..((((((.((((((((.........)))))))))))))))).-.)))))......-..................-------------------- ( -26.50)
>consensus
_____C_GCCGCUUGACAAAUGCAACCGCCAACAAUGACGCAGUUGGUGGUGCAUUUCU_UCGGCAUUUCUU_UAAAAAUAAAUUUAUGUG____________________
.......((((...((..((((((.((((((((.........))))))))))))))))...)))).............................................. (-21.93 = -22.40 +   0.47)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,582,518 – 15,582,624
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.84
Mean single sequence MFE -26.04
Consensus MFE -17.27
Energy contribution -17.30
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -1.80
Structure conservation index 0.66
SVM decision value 0.87
SVM RNA-class probability 0.871100
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15582518 106 - 20766785
--AGCAA-AGCGAAGGCGGCCACAUAAAUUUAUUUUUA-AAGAAAUGCCGA-AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCCACCGAUCCA
--.....-..((..((((((........((((....))-)).....)))((-..(((((((((.(((((.........))))).)).))))))).))..)))..))..... ( -28.82)
>DroVir_CAF1 522135 83 - 1
--------------------CACAUAAAUUUAUUUUUA-AAGAAAUGCCGAAAGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGGC-------
--------------------..................-.......((((..(.(((((((((.(((((.........))))).)).))))))).)....))))------- ( -23.60)
>DroWil_CAF1 698972 96 - 1
---------ACAAAGGCGGCCACAUAAAUUUAUUUUUA-AAGAAAUGCCGAAAGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAGUUGUCAAACGACUG-----
---------......((((((..........(((((..-..)))))(((((.....(((((........))))).....)))))))))))(((((.....))))).----- ( -24.80)
>DroMoj_CAF1 585058 84 - 1
--------------------CACAUAAAUUUAUUUUUAAAAGAAAUGCCCAAAGAAAUGCACCACCAACUGCGUCUUUGUUGGCGGUUGCAUUUGUCAAGCGGC-------
--------------------..........................((((..(.(((((((((.(((((.........))))).)).))))))).)...).)))------- ( -20.30)
>DroAna_CAF1 350696 107 - 1
CCAGCGAAGGCGGCGGCGGGCACAUAAAUUUAUUUUUA-AAGAAAUGCCGA-AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCGUUUGUCA--CAAGCGGGGCA
((.((....)).((((((......((((......))))-......))))((-..(((((((((.(((((.........))))).)).))))))).)).--...)))).... ( -32.50)
>DroPer_CAF1 383766 89 - 1
--------------------CACAUAAAUUUAUUUUUA-AAGAAAUGCCGA-GGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGGCAGCGGGA
--------------------..................-..(...(((((.-.((((((((((.(((((.........))))).)).))))))..))...))))).).... ( -26.20)
>consensus
____________________CACAUAAAUUUAUUUUUA_AAGAAAUGCCGA_AGAAAUGCACCACCAACUGCGUCAUUGUUGGCGGUUGCAUUUGUCAAGCGAC_G_____
..............................((((((.....)))))).......(((((((((.(((((.........))))).)).)))))))................. (-17.27 = -17.30 +   0.03)

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 11:28:21 2006