Locus 593

Sequence ID X_DroMel_CAF1
Location 1,663,934 – 1,664,168
Length 234
Max. P 0.996632
window945 window946 window947 window948 window949

overview

Window 5

Location 1,663,934 – 1,664,040
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.74
Mean single sequence MFE -32.23
Consensus MFE -22.88
Energy contribution -25.12
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.71
SVM decision value 1.93
SVM RNA-class probability 0.983113
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1663934 106 + 22224390
GGAAUUCCACAGCGAAACGGGCUGUAGUAAUGAAGAUAACAUUUCCUGUUGUCAGCAUUUGCAAAGUUGGACAAAGCCAGCUCGCAGCCC--CACACUCGCACCCUUG------------
((....))...((((...(((((((.((((((..(((((((.....)))))))..)).))))..((((((......)))))).)))))))--.....)))).......------------ ( -36.60)
>DroSim_CAF1 1897 118 + 1
GGAAUUCCAGAGCGAAACGGGCUGUAGUAAUGAAGAUAACAUUUCCUGUUGUCAGCAUUUGCAAAGUUGGACAAAGCCAGCUCGCAGCCC--CACAUCCGCACCCUUGCGUCCUCGCAUC
((....))...((((...(((((((.((((((..(((((((.....)))))))..)).))))..((((((......)))))).)))))))--......((((....))))...))))... ( -40.90)
>DroEre_CAF1 9619 80 + 1
GGAAUUCCAAAGCGAAACGGGCUGUAGUAAUGAAGAUAACAUUUCCUGUUGUCAGCAUUUGCAAAGUUGGACAAAGCCAG----------------------------------------
((...(((((.(((((....(((.((....))..(((((((.....)))))))))).)))))....))))).....))..---------------------------------------- ( -18.50)
>DroYak_CAF1 2119 116 + 1
GGAAUUCCAGAGCGAAACGGGCUGUAGUAAUGAAGAUAACAUUUCCUGUUGUCAGCAUUUGCAAAGUUGGACAAAGCCAGCUCGCAGCCCCCCACAUCCACAUCCA--CAUC--CGCAUC
(((.(((......)))..(((((((.((((((..(((((((.....)))))))..)).))))..((((((......)))))).)))))))......))).......--....--...... ( -32.90)
>consensus
GGAAUUCCAGAGCGAAACGGGCUGUAGUAAUGAAGAUAACAUUUCCUGUUGUCAGCAUUUGCAAAGUUGGACAAAGCCAGCUCGCAGCCC__CACAUCCGCACCCU______________
((....))..........(((((((.((((((..(((((((.....)))))))..)).))))..((((((......)))))).))))))).............................. (-22.88 = -25.12 +   2.25)

alignment

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secondary structure

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Window 6

Location 1,664,014 – 1,664,112
Length 98
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 78.20
Mean single sequence MFE -31.77
Consensus MFE -17.54
Energy contribution -18.73
Covariance contribution 1.20
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.55
SVM decision value 0.03
SVM RNA-class probability 0.550800
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1664014 98 + 22224390
CUCGCAGCCC--CACACUCGCACCCUUG----------------CAUCCUGGUAUCCUGGCACUCCACGCGCUUCAAACUUUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGGA
.........(--(......(((....))----------------).((((..(((..((((((((((...((((((.......))))))))-).)))))))..)))..).))).)). ( -29.00)
>DroSim_CAF1 1977 112 + 1
CUCGCAGCCC--CACAUCCGCACCCUUGCGUCCUCGCAUCCUCGCAUCCUCGCAUCCUGGCACUCC--GCGCUUCAAACUUUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGGA
..........--....((((((....)))((((((((......((......))....(((((((((--(.((((((.......))))))))-).)))))))..))))...))))))) ( -38.80)
>DroYak_CAF1 2199 111 + 1
CUCGCAGCCCCCCACAUCCACAUCCA--CAUC--CGCAUCCUCGCAUCCUCGCACCCUCGCACUUC--UCGCUUCAAAGUUUAUGAAGCUGGGAAGUGGCAAAAUGAAACGGACGGA
..........................--..((--((..(((..((......))......(((((((--((((((((.......)))))).))))))).))..........))))))) ( -27.50)
>consensus
CUCGCAGCCC__CACAUCCGCACCCUUGC_UC__CGCAUCCUCGCAUCCUCGCAUCCUGGCACUCC__GCGCUUCAAACUUUAUGAAGCUG_GAAGUGCCAAAGUGAAACGGACGGA
.......................((..........((......)).(((...(((..(((((((.(....((((((.......))))))...).)))))))..)))....))).)). (-17.54 = -18.73 +   1.20)

alignment

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secondary structure

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Window 7

Location 1,664,040 – 1,664,134
Length 94
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 78.18
Mean single sequence MFE -32.10
Consensus MFE -21.11
Energy contribution -21.33
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -2.14
Structure conservation index 0.66
SVM decision value 1.44
SVM RNA-class probability 0.954213
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1664040 94 + 22224390
----CAUCCUGGUAUCCUGGCACUCCACGCGCUUCAAACUUUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGGACUGUAACAGUUUUUCGAUUGCU------------------
----.............((((((((((...((((((.......))))))))-).))))))).((..(..((((.((((((...)))))))))).)..))------------------ ( -28.30)
>DroSim_CAF1 2015 96 + 1
CUCGCAUCCUCGCAUCCUGGCACUCC--GCGCUUCAAACUUUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGGACUGUAACAGUUUUUCGAUUGUU------------------
...((((((((.(((..(((((((((--(.((((((.......))))))))-).)))))))..))).....)).))).)))(((((((....)))))))------------------ ( -32.00)
>DroYak_CAF1 2235 115 + 1
CUCGCAUCCUCGCACCCUCGCACUUC--UCGCUUCAAAGUUUAUGAAGCUGGGAAGUGGCAAAAUGAAACGGACGGACUGUUACAGUUUUUCGAUUGCUGAAAAAGGAGCGAAAGUU
.((((.((((..........((((((--((((((((.......)))))).))))))))((((...(((((.(((.....)))...)))))....))))......))))))))..... ( -36.00)
>consensus
CUCGCAUCCUCGCAUCCUGGCACUCC__GCGCUUCAAACUUUAUGAAGCUG_GAAGUGCCAAAGUGAAACGGACGGACUGUAACAGUUUUUCGAUUGCU__________________
...........(((...(((((((.(....((((((.......))))))...).)))))))........((((.((((((...))))))))))..)))................... (-21.11 = -21.33 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,664,040 – 1,664,134
Length 94
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 78.18
Mean single sequence MFE -33.01
Consensus MFE -28.35
Energy contribution -29.13
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.29
Structure conservation index 0.86
SVM decision value 2.73
SVM RNA-class probability 0.996632
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1664040 94 - 22224390
------------------AGCAAUCGAAAAACUGUUACAGUCCGUCCGUUUCACUUUGGCACUUC-CAGCUUCAUAAAGUUUGAAGCGCGUGGAGUGCCAGGAUACCAGGAUG----
------------------............((((...)))).(((((.......(((((((((((-(.((((((.......))))))..).)))))))))))......)))))---- ( -30.62)
>DroSim_CAF1 2015 96 - 1
------------------AACAAUCGAAAAACUGUUACAGUCCGUCCGUUUCACUUUGGCACUUC-CAGCUUCAUAAAGUUUGAAGCGC--GGAGUGCCAGGAUGCGAGGAUGCGAG
------------------.....(((....((((...)))).(((((.((.((..((((((((((-..((((((.......))))))..--))))))))))..)).)))))))))). ( -34.60)
>DroYak_CAF1 2235 115 - 1
AACUUUCGCUCCUUUUUCAGCAAUCGAAAAACUGUAACAGUCCGUCCGUUUCAUUUUGCCACUUCCCAGCUUCAUAAACUUUGAAGCGA--GAAGUGCGAGGGUGCGAGGAUGCGAG
.....(((((((((.....(((..(((...((((...))))...)).........((((.(((((...((((((.......))))))..--))))))))))..)))))))).)))). ( -33.80)
>consensus
__________________AGCAAUCGAAAAACUGUUACAGUCCGUCCGUUUCACUUUGGCACUUC_CAGCUUCAUAAAGUUUGAAGCGC__GGAGUGCCAGGAUGCGAGGAUGCGAG
..............................((((...)))).(((((....((..((((((((((...((((((.......))))))....))))))))))..))...))))).... (-28.35 = -29.13 +   0.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,664,076 – 1,664,168
Length 92
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.53
Mean single sequence MFE -31.12
Consensus MFE -19.96
Energy contribution -21.15
Covariance contribution 1.19
Combinations/Pair 1.10
Mean z-score -2.14
Structure conservation index 0.64
SVM decision value 1.40
SVM RNA-class probability 0.950418
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1664076 92 + 22224390
UUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGG---ACUGUAACAGUUUUUCGAUUGCU-------------------CUUGCACUAAAUCAGCUUCAUUUUGG-----GCUCCACC
..(((((((((-(.(((((...((..(..((((.((---((((...)))))))))).)..))-------------------...)))))...))))))))))...((-----......)) ( -28.10)
>DroSim_CAF1 2053 92 + 1
UUAUGAAGCUG-GAAGUGCCAAAGUGAAACGGACGG---ACUGUAACAGUUUUUCGAUUGUU-------------------CUUGCACUAAAUCAGCUUCAUUUUGG-----GCUCCACC
..(((((((((-(.(((((..(((...((((((.((---((((...)))))))))).))...-------------------))))))))...))))))))))...((-----......)) ( -26.10)
>DroEre_CAF1 9725 113 + 1
UUAUGGAGCUG-GAAGUGCCAAAGUGAAACGGACGGACGACUGUUACACUUUUCCGAUUGCUCAA-AAGCAGCGAAAGUUCCACGCACUAAAUCAGCUUCAUUUUUG-----GCUCCGCU
....(((((..-((((((..((((((.(((((.(....).))))).))))))...(((((((...-.)))(((....)))..........)))).....))))))..-----)))))... ( -34.50)
>DroYak_CAF1 2273 117 + 1
UUAUGAAGCUGGGAAGUGGCAAAAUGAAACGGACGG---ACUGUUACAGUUUUUCGAUUGCUGAAAAAGGAGCGAAAGUUCCACGCACUAAAUUAGCUUCAUUUUUGGGGGAGCUCUACU
..((((((((((..((((((((...(((((.(((..---...)))...)))))....)))).......(((((....)))))...))))...))))))))))....(((....))).... ( -35.80)
>consensus
UUAUGAAGCUG_GAAGUGCCAAAGUGAAACGGACGG___ACUGUAACAGUUUUUCGAUUGCU___________________CACGCACUAAAUCAGCUUCAUUUUGG_____GCUCCACC
..(((((((((...(((((..........(((.(((...((((...))))...))).)))........(((((....)))))..)))))....))))))))).................. (-19.96 = -21.15 +   1.19)

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 09:48:48 2006