Locus 1188

Sequence ID 3R_DroMel_CAF1
Location 3,578,953 – 3,579,105
Length 152
Max. P 0.691084
window1944 window1945 window1946

overview

Window 4

Location 3,578,953 – 3,579,065
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.97
Mean single sequence MFE -23.62
Consensus MFE -13.94
Energy contribution -13.56
Covariance contribution -0.38
Combinations/Pair 1.47
Mean z-score -1.44
Structure conservation index 0.59
SVM decision value 0.02
SVM RNA-class probability 0.545671
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578953 112 + 27905053
UUC--------GCAACAAUUGCUUUCGGUUAGACAAUUGCCGCCGAAAAGCAAUCUAAAAUUUUCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUAGAAGUACCAGCACCAAUGCCUG
...--------((.....(((((((((((............)))).)))))))((((.......((((((................))))))....)))).......))........... ( -25.09)
>DroSec_CAF1 29888 93 + 1
UUC--------GCAACAAUUGCUUUCGGUUAGACAAUCGCCGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA-------------------
...--------((....((((.(((((((..(.....)...)))))))..))))..........((((((................))))))...))....------------------- ( -19.99)
>DroSim_CAF1 30370 93 + 1
UUC--------GCAACAAUUGCCUUCGGUUAGACAAUCGCCGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA-------------------
...--------((....((((..((((((..(.....)...))))))...))))..........((((((................))))))...))....------------------- ( -19.09)
>DroEre_CAF1 35244 94 + 1
UUC--------GCAACAAUUGCUUUCGGUUAGACAAUCGCCGCCGAAAAGCAAUCUAAAAUUGCCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUGGCA------------------G
...--------((....((((((((((((..(.....)...)))).)))))))).....((((.((((((................)))))).)))).)).------------------. ( -28.19)
>DroYak_CAF1 22123 94 + 1
CUC--------GCAACAAUUGCUUUCAGUUAGACAAUCGCCGUCGAGAAGCAAUCUAAAAUUUUCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUGCGA------------------G
(((--------(((...((((((((......(((.......)))..))))))))..........((((((................))))))....)))))------------------) ( -25.59)
>DroAna_CAF1 25705 100 + 1
UUUUCAUCGGGGAAAAACUUGCCCCCAAACGGACAAUCAACUGUGAAAACCAAUCAAAAAUUUUCCGCCCAAAAACUGCAUUAAGUGGGCGGUGAGCC-CA-------------------
(((((...((((..........))))..((((........)))))))))...........(((.((((((....(((......))))))))).)))..-..------------------- ( -23.80)
>consensus
UUC________GCAACAAUUGCUUUCGGUUAGACAAUCGCCGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA___________________
...................((((((((((..(.....)...)))))))................((((((................))))))...)))...................... (-13.94 = -13.56 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,578,953 – 3,579,065
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.97
Mean single sequence MFE -29.12
Consensus MFE -18.99
Energy contribution -18.57
Covariance contribution -0.41
Combinations/Pair 1.33
Mean z-score -1.33
Structure conservation index 0.65
SVM decision value 0.33
SVM RNA-class probability 0.691084
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578953 112 - 27905053
CAGGCAUUGGUGCUGGUACUUCUACUGGCCACCCCUUUAAUGCAGUUUUCGGGUGGAAAAUUUUAGAUUGCUUUUCGGCGGCAAUUGUCUAACCGAAAGCAAUUGUUGC--------GAA
...((((((((((..(((....)))..).)))).....))))).((((((((.((((........(((((((.......))))))).)))).)))))))).........--------... ( -34.00)
>DroSec_CAF1 29888 93 - 1
-------------------UGCUGCUGGCCACCCCUUUAAUGCAGUUUUUGGGUGGGAAAUUUUAGAUUGGUUUUCGGCGGCGAUUGUCUAACCGAAAGCAAUUGUUGC--------GAA
-------------------.((.((...((((((................)))))).........(((((.(((((((.(((....)))...)))))))))))))).))--------... ( -24.49)
>DroSim_CAF1 30370 93 - 1
-------------------UGCUGCUGGCCACCCCUUUAAUGCAGUUUUUGGGUGGGAAAUUUUAGAUUGGUUUUCGGCGGCGAUUGUCUAACCGAAGGCAAUUGUUGC--------GAA
-------------------.(((((((.((((((................))))))((((((.......)))))))))))))((((((((......)))))))).....--------... ( -28.79)
>DroEre_CAF1 35244 94 - 1
C------------------UGCCACUGGCCACCCCUUUAAUGCAGUUUUCGGGUGGGCAAUUUUAGAUUGCUUUUCGGCGGCGAUUGUCUAACCGAAAGCAAUUGUUGC--------GAA
.------------------(((.((((.((((((................)))))).))......(((((((((.(((.(((....)))...)))))))))))))).))--------).. ( -29.89)
>DroYak_CAF1 22123 94 - 1
C------------------UCGCACUGGCCACCCCUUUAAUGCAGUUUUCGGGUGGAAAAUUUUAGAUUGCUUCUCGACGGCGAUUGUCUAACUGAAAGCAAUUGUUGC--------GAG
(------------------(((((....((((((................)))))).........((((((((.(((..(((....)))....)))))))))))..)))--------))) ( -26.39)
>DroAna_CAF1 25705 100 - 1
-------------------UG-GGCUCACCGCCCACUUAAUGCAGUUUUUGGGCGGAAAAUUUUUGAUUGGUUUUCACAGUUGAUUGUCCGUUUGGGGGCAAGUUUUUCCCCGAUGAAAA
-------------------.(-(((...(((((((..............))))))).......(..((((.......))))..)..))))..(((((((........)))))))...... ( -31.14)
>consensus
___________________UGCUACUGGCCACCCCUUUAAUGCAGUUUUCGGGUGGAAAAUUUUAGAUUGCUUUUCGGCGGCGAUUGUCUAACCGAAAGCAAUUGUUGC________GAA
............................((((((................)))))).........(((((.(((((((.(((....)))...))))))))))))................ (-18.99 = -18.57 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,578,985 – 3,579,105
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.12
Mean single sequence MFE -22.21
Consensus MFE -16.80
Energy contribution -16.56
Covariance contribution -0.24
Combinations/Pair 1.38
Mean z-score -1.29
Structure conservation index 0.76
SVM decision value -0.01
SVM RNA-class probability 0.530829
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578985 120 + 27905053
CGCCGAAAAGCAAUCUAAAAUUUUCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUAGAAGUACCAGCACCAAUGCCUGUGCCGUAAAUUAAUAUGGUGGCGAAACUCUAAAAUUGAAA
((((.....(((.((((.......((((((................))))))....)))).......(((....))).)))((((((......))))))))))................. ( -25.89)
>DroSec_CAF1 29920 99 + 1
CGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA---------------------CCGUAAAUUAAUAUGGUGGCGAAAGUCUAAAAUUGAAA
((((....................((((((................))))))........(---------------------(((((......))))))))))................. ( -21.59)
>DroSim_CAF1 30402 99 + 1
CGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA---------------------CCGUAAAUUAAUAUGGUGGCGAAAGUCUAAAAUUGAAA
((((....................((((((................))))))........(---------------------(((((......))))))))))................. ( -21.59)
>DroEre_CAF1 35276 102 + 1
CGCCGAAAAGCAAUCUAAAAUUGCCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUGGCA------------------GUGUCGUAAAUUAAUAUGGUGGCGAAACUCUAAAAUUGAAA
.((((....(((((.....)))))((((((................))))))....))))(------------------((.((((...(......)...)))).)))............ ( -22.59)
>DroYak_CAF1 22155 102 + 1
CGUCGAGAAGCAAUCUAAAAUUUUCCACCCGAAAACUGCAUUAAAGGGGUGGCCAGUGCGA------------------GUGCCGUAAAUUAAUAUGGUGGCGAAACUGUAAAAUUGAAA
..((((..................((((((................)))))).((((.((.------------------.(((((((......))))))).))..)))).....)))).. ( -20.99)
>DroAna_CAF1 25745 98 + 1
CUGUGAAAACCAAUCAAAAAUUUUCCGCCCAAAAACUGCAUUAAGUGGGCGGUGAGCC-CA---------------------CCAUAAAUUAAUGUGCUGGCAAAACUAUAAAAUUGAAA
..((....))...((((.......((((((....(((......)))))))))...(((-..---------------------.((((......))))..)))............)))).. ( -20.60)
>consensus
CGCCGAAAACCAAUCUAAAAUUUCCCACCCAAAAACUGCAUUAAAGGGGUGGCCAGCAGCA_____________________CCGUAAAUUAAUAUGGUGGCGAAACUCUAAAAUUGAAA
(((((...................((((((................))))))..............................(((((......))))))))))................. (-16.80 = -16.56 +  -0.24)

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 10:03:11 2006