Locus 334

Sequence ID X_DroMel_CAF1
Location 1,054,232 – 1,054,366
Length 134
Max. P 0.999964
window506 window507 window508 window509

overview

Window 6

Location 1,054,232 – 1,054,342
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.77
Mean single sequence MFE -33.74
Consensus MFE -31.07
Energy contribution -32.15
Covariance contribution 1.08
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.92
SVM decision value 2.35
SVM RNA-class probability 0.992788
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1054232 110 + 22224390
----------UGAAAAUGCGAAUCUGCCAGUGAGUGCGGAAGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
----------..............(((((((((((((((.(((.((((((..(((((((.......)))))))..)))....)))))).)))))))).............)))))))... ( -35.01)
>DroSec_CAF1 3177 110 + 1
----------UGGAAAUGCGAAUCUGCCAGUGAGUGCGGAAGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
----------..............(((((((((((((((.(((.((((((..(((((((.......)))))))..)))....)))))).)))))))).............)))))))... ( -35.01)
>DroSim_CAF1 4112 110 + 1
----------UGGAAAUGCGAAUCUGCCAGUGAGUGCGGAAGCUGCCGACCGCUUUUUAAUUUGAAUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
----------..............(((((((((((((((.(((.((((((..(((((((.......)))))))..)))....)))))).)))))))).............)))))))... ( -35.01)
>DroEre_CAF1 3198 109 + 1
GG------AGUGGGAAUGGGAAUCUGCCA--GAGUGCGGAAGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAG---UCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
..------................(((((--((((((((.(((.(((..((((((........))))))...(---....).)))))).))))))))...............)))))... ( -31.76)
>DroYak_CAF1 5339 117 + 1
GAAACUGCAAUGGGAAUGGGAAUCUGCCAAAGAGUGCGGAAGCUGCCAACCGCUUUUUAAUUUGAGUGGAAAG---UCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
........................((((((...((((((.(((.(((..((((((........))))))...(---....).)))))).))))))(((.........))).))))))... ( -31.90)
>consensus
__________UGGAAAUGCGAAUCUGCCAGUGAGUGCGGAAGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAA
........................(((((((((((((((.(((.(((..((((((........))))))...((.....)).)))))).)))))))).............)))))))... (-31.07 = -32.15 +   1.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,054,232 – 1,054,342
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.77
Mean single sequence MFE -31.24
Consensus MFE -28.94
Energy contribution -29.58
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.64
Structure conservation index 0.93
SVM decision value 4.35
SVM RNA-class probability 0.999878
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1054232 110 - 22224390
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCUUCCGCACUCACUGGCAGAUUCGCAUUUUCA----------
.(.((((((((((.........)))))((((.(((...(((((((..((((.............))))..)))))))))).))))......))))).)............---------- ( -32.32)
>DroSec_CAF1 3177 110 - 1
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCUUCCGCACUCACUGGCAGAUUCGCAUUUCCA----------
.(.((((((((((.........)))))((((.(((...(((((((..((((.............))))..)))))))))).))))......))))).)............---------- ( -32.32)
>DroSim_CAF1 4112 110 - 1
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCAUUCAAAUUAAAAAGCGGUCGGCAGCUUCCGCACUCACUGGCAGAUUCGCAUUUCCA----------
.(.((((((((((.........)))))((((.(((...(((((((..((((.............))))..)))))))))).))))......))))).)............---------- ( -32.32)
>DroEre_CAF1 3198 109 - 1
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGA---CUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCUUCCGCACUC--UGGCAGAUUCCCAUUCCCACU------CC
.(.((((((((((.........)))))((((.((((((..(((.---((((.............)))))))..))).))).))))....--))))).)..............------.. ( -29.42)
>DroYak_CAF1 5339 117 - 1
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGA---CUUUCCACUCAAAUUAAAAAGCGGUUGGCAGCUUCCGCACUCUUUGGCAGAUUCCCAUUCCCAUUGCAGUUUC
.(.((((((((((.........))))(((((.((((((..(((.---((((.............)))))))..))).))).)))))....)))))).)...................... ( -29.82)
>consensus
UUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCUUCCGCACUCACUGGCAGAUUCGCAUUUCCA__________
.(.((((((((((.........)))))((((.(((...((((((((.((((.............)))).))))))))))).))))......))))).)...................... (-28.94 = -29.58 +   0.64)

alignment

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secondary structure

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Window 8

Location 1,054,262 – 1,054,366
Length 104
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 94.18
Mean single sequence MFE -36.42
Consensus MFE -32.33
Energy contribution -33.13
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -3.57
Structure conservation index 0.89
SVM decision value 4.56
SVM RNA-class probability 0.999920
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1054262 104 + 22224390
AGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUAC-------CAUCCAUUGCGGCAGCUGA
.(((..((((..(((((((.......)))))))..))))...)))(((((((((((((.........)))).(((.........)-------)).....)))))))))... ( -35.00)
>DroSec_CAF1 3207 104 + 1
AGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUAC-------CAGCCAUUGCGGCAGCUGA
.(((..((((..(((((((.......)))))))..))))...)))(((((((((((((.........)))).((((.........-------..)))).)))))))))... ( -38.60)
>DroSim_CAF1 4142 104 + 1
AGCUGCCGACCGCUUUUUAAUUUGAAUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUAC-------CAGCCAUUGCGGCAGCUGA
.(((..((((..(((((((.......)))))))..))))...)))(((((((((((((.........)))).((((.........-------..)))).)))))))))... ( -38.60)
>DroEre_CAF1 3230 108 + 1
AGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAG---UCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUACCAGUUACCAGCCAUUGCGGCAGCUGA
((((((((.((((((........))))))....---......((((.(((((.(((((.........)))))))))))(((......)))....)))....)))))))).. ( -35.50)
>DroYak_CAF1 5379 101 + 1
AGCUGCCAACCGCUUUUUAAUUUGAGUGGAAAG---UCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUAC-------CAGCCAUUGCGGCAGCUUA
....(((..((((((........))))))...(---....).)))(((((((((((((.........)))).((((.........-------..)))).)))))))))... ( -34.40)
>consensus
AGCUGCCGACCGCUUUUUAAUUUGAGUGGAAAGUAGUCGACAGGCGCUGCCGCAUUUCAAAAUUAUAGAAAUUGGCACAAUUUAC_______CAGCCAUUGCGGCAGCUGA
.(((..((((..(((((((.......)))))))..))))...)))(((((((((((((.........)))).((((..................)))).)))))))))... (-32.33 = -33.13 +   0.80)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,054,262 – 1,054,366
Length 104
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 94.18
Mean single sequence MFE -38.29
Consensus MFE -35.33
Energy contribution -36.17
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -4.18
Structure conservation index 0.92
SVM decision value 4.96
SVM RNA-class probability 0.999964
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1054262 104 - 22224390
UCAGCUGCCGCAAUGGAUG-------GUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCU
...((((((((......((-------(((.....)))))(((((.........)))))))))))))((.(((((((..((((.............))))..))))))))). ( -39.92)
>DroSec_CAF1 3207 104 - 1
UCAGCUGCCGCAAUGGCUG-------GUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCU
...((((((((..((((..-------.........))))(((((.........)))))))))))))((.(((((((..((((.............))))..))))))))). ( -40.52)
>DroSim_CAF1 4142 104 - 1
UCAGCUGCCGCAAUGGCUG-------GUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCAUUCAAAUUAAAAAGCGGUCGGCAGCU
...((((((((..((((..-------.........))))(((((.........)))))))))))))((.(((((((..((((.............))))..))))))))). ( -40.52)
>DroEre_CAF1 3230 108 - 1
UCAGCUGCCGCAAUGGCUGGUAACUGGUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGA---CUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCU
...((((((((..((((..................))))(((((.........)))))))))))))((.((((((---((....................)))))))))). ( -36.02)
>DroYak_CAF1 5379 101 - 1
UAAGCUGCCGCAAUGGCUG-------GUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGA---CUUUCCACUCAAAUUAAAAAGCGGUUGGCAGCU
...((((((((..((((..-------.........))))(((((.........)))))))))))))((.((((((---((....................)))))))))). ( -34.45)
>consensus
UCAGCUGCCGCAAUGGCUG_______GUAAAUUGUGCCAAUUUCUAUAAUUUUGAAAUGCGGCAGCGCCUGUCGACUACUUUCCACUCAAAUUAAAAAGCGGUCGGCAGCU
...((((((((..((((..................))))(((((.........)))))))))))))((.((((((((.((((.............)))).)))))))))). (-35.33 = -36.17 +   0.84)

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 09:42:01 2006