Locus 1957

Sequence ID 2L_DroMel_CAF1
Location 5,283,673 – 5,283,793
Length 120
Max. P 0.960076
window3167 window3168 window3169

overview

Window 7

Location 5,283,673 – 5,283,769
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.70
Mean single sequence MFE -23.62
Consensus MFE -14.93
Energy contribution -15.15
Covariance contribution 0.22
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.63
SVM decision value 0.88
SVM RNA-class probability 0.873148
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5283673 96 - 22407834
GCUGCAAGUUGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUA----GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCGAACGA------------G
(((((.....))))).(((((((((((((....)))))(..((.(----((((((((....)))))))))))..)..............)))))..)))------------. ( -29.90)
>DroPse_CAF1 67639 88 - 1
--------UUGGAGCUGGCUGCCACGACUUCUAAGUCGGUUACUA----GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCCAACGU------------G
--------.....(.(((((....(((((....)))))(..((.(----((((((((....)))))))))))..)...............))))).)..------------. ( -22.20)
>DroSim_CAF1 65590 91 - 1
-----AGGCCGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUA----GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCGAACGA------------G
-----...........(((((((((((((....)))))(..((.(----((((((((....)))))))))))..)..............)))))..)))------------. ( -24.00)
>DroWil_CAF1 15190 86 - 1
---------UCCAACUG-CAGCAGCGGCUUCUAACUCGGUUACUAGUUAGAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCAU----------------U
---------.(((((((-(....))))..(((((((.(....).)))))))((((((....)))))).....................))))...----------------. ( -17.50)
>DroAna_CAF1 44533 95 - 1
-------------UUUUCGUGGCACGACUUCUAAGUCGGUUACUA----GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCGAACAACGACGACGUCGAG
-------------.....(((((.(((((....))))))))))((----((((((((....))))))))))................(((((((...........))))))) ( -25.90)
>DroPer_CAF1 69203 88 - 1
--------UUGGAGCUGGCUGCCACGACUUCUAAGUCGGUUACUA----GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCCAACGU------------G
--------.....(.(((((....(((((....)))))(..((.(----((((((((....)))))))))))..)...............))))).)..------------. ( -22.20)
>consensus
________UUGCAGCUGCCUGCCACGACUUCUAAGUCGGUUACUA____GAUGCAAUAAUAAUUGCAUUUGUCCCACUUUACUUUCACUUGGCGAACGA____________G
....................(((((((((....)))))...........((((((((....))))))))....................))))................... (-14.93 = -15.15 +   0.22)

alignment

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secondary structure

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Window 8

Location 5,283,700 – 5,283,793
Length 93
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 81.28
Mean single sequence MFE -24.93
Consensus MFE -14.80
Energy contribution -15.28
Covariance contribution 0.47
Combinations/Pair 1.10
Mean z-score -2.24
Structure conservation index 0.59
SVM decision value 0.46
SVM RNA-class probability 0.746896
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5283700 93 + 22407834
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCGCGAAACUGCAACUUGCAGCCUAUGCAGUAUGCAGUAUGCAGUU
.....(((((((....)))))))...((...(((((....)))))..))(((..(((((((((.(((.....)))))).)))))).))).... ( -27.60)
>DroPse_CAF1 67666 76 + 1
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCAGCCAGCUCCAA-----------------AGCCAGCCAGCAGUU
(((..(((((((....)))))))...((...(((((....)))))((((.....(((....-----------------)))..)))))).))) ( -16.80)
>DroSec_CAF1 59327 84 + 1
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCGCGAAACUGCAGCCU---------GCAGUAUGCAGUUUGCAGUU
.....(((((((....)))))))...((..((((((....))))).)..))..((((((((.((---------((.....)))).)))))))) ( -29.30)
>DroSim_CAF1 65617 84 + 1
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCGCGAAACUGCGGCCU---------GCAGUAUGCAGUUUGCAGUU
.....(((((((....)))))))...((..((((((....))))).)..))..(((((((..((---------((.....))))..))))))) ( -28.60)
>DroEre_CAF1 55283 91 + 1
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCGCGAAACUGCAGCUUGCGGCCU--GCAGCUUGCAGUUUGCAGUU
.....(((((((....)))))))...((...(((((....)))))..))((.(((((((((((.((.....--))))).)))))))))).... ( -30.50)
>DroPer_CAF1 69230 76 + 1
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCAGCCAGCUCCAA-----------------AGCCAGCCAGCAGUU
(((..(((((((....)))))))...((...(((((....)))))((((.....(((....-----------------)))..)))))).))) ( -16.80)
>consensus
GACAAAUGCAAUUAUUAUUGCAUCUAGUAACCGACUUAGAAGUCGUGGCGCGAAACUGCAAC_U_________GCAGUAUGCAGUUUGCAGUU
.....(((((((....)))))))...((...(((((....)))))..)).....((((((...................))))))........ (-14.80 = -15.28 +   0.47)

alignment

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secondary structure

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Window 9

Location 5,283,700 – 5,283,793
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 81.28
Mean single sequence MFE -28.68
Consensus MFE -19.26
Energy contribution -19.15
Covariance contribution -0.11
Combinations/Pair 1.17
Mean z-score -3.61
Structure conservation index 0.67
SVM decision value 1.51
SVM RNA-class probability 0.960076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5283700 93 - 22407834
AACUGCAUACUGCAUACUGCAUAGGCUGCAAGUUGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
....((..((((((.((((((.....))).)))))))))...))....(((((....))))).....((((((((((....)))))))))).. ( -28.90)
>DroPse_CAF1 67666 76 - 1
AACUGCUGGCUGGCU-----------------UUGGAGCUGGCUGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
....((.(((..(((-----------------....)))..)))))..(((((....))))).....((((((((((....)))))))))).. ( -26.20)
>DroSec_CAF1 59327 84 - 1
AACUGCAAACUGCAUACUGC---------AGGCUGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
(((((((..((((.....))---------))..)))))))........(((((....))))).....((((((((((....)))))))))).. ( -30.50)
>DroSim_CAF1 65617 84 - 1
AACUGCAAACUGCAUACUGC---------AGGCCGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
((((((...((((.....))---------))...))))))........(((((....))))).....((((((((((....)))))))))).. ( -27.50)
>DroEre_CAF1 55283 91 - 1
AACUGCAAACUGCAAGCUGC--AGGCCGCAAGCUGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
....((((((((((.(((((--.....)).))))))))))).))....(((((....))))).....((((((((((....)))))))))).. ( -32.80)
>DroPer_CAF1 69230 76 - 1
AACUGCUGGCUGGCU-----------------UUGGAGCUGGCUGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
....((.(((..(((-----------------....)))..)))))..(((((....))))).....((((((((((....)))))))))).. ( -26.20)
>consensus
AACUGCAAACUGCAUACUGC_________A_GCUGCAGUUUCGCGCCACGACUUCUAAGUCGGUUACUAGAUGCAAUAAUAAUUGCAUUUGUC
....(((((((((.....................))))))).))....(((((....))))).....((((((((((....)))))))))).. (-19.26 = -19.15 +  -0.11)

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 10:15:58 2006