Locus 4511

Sequence ID 3R_DroMel_CAF1
Location 11,969,837 – 11,970,014
Length 177
Max. P 0.965995
window7369 window7370 window7371

overview

Window 9

Location 11,969,837 – 11,969,955
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 73.23
Mean single sequence MFE -40.98
Consensus MFE -33.80
Energy contribution -34.47
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -1.32
Structure conservation index 0.82
SVM decision value 1.59
SVM RNA-class probability 0.965995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11969837 118 + 27905053
UAAUUGGCAUGAACGCCACGGUCACCGGCUGGGGUCGUCUCAGCGAGGGCGGCACCCUGCCCUCCGUCCUCCAAGAGGUGAGUGUUAACACGACUUUAAGCUUCAUUUUUAGAAUUCA
.....(((......)))(((.(((((.((((((.....))))))((((((((....))))))))............))))).)))................................. ( -38.40)
>DroVir_CAF1 85122 96 + 1
UGAUUGGCAUGAAUGCCACGGUCACCGGCUGGGGUCGCCUCAGCGAGGGCGGUACGCUGCCCUCGGUGCUGCAGGAGGUAAGUGG-------AGUU--AGCACAA-------------
....(((((....)))))(((.((((.(((((((...)))))))((((((((....)))))))))))))))..........(((.-------....--..)))..------------- ( -43.60)
>DroPse_CAF1 80411 93 + 1
UAAUUGGCAUGAAUGCCACGGUCACCGGCUGGGGUCGUCUGAGCGAGGGCGGCACCCUGCCCUCGGUCCUCCAAGAGGUGAGUGCUUG---------G----------------UGGU
....(((((....)))))((.(((((...(((((......((.(((((((((....))))))))).)))))))...))))).))....---------.----------------.... ( -40.40)
>DroGri_CAF1 82817 101 + 1
UGAUUGGCAUGAAUGCCACCGUCACCGGCUGGGGUCGUCUCAGUGAGGGCGGUACGCUGCCGUCGGUGCUGCAGGAGGUAAGUGCA--UGCGACUG--GUCUCAA-------------
.(((..(((((..((((.((((((((.((((((.....))))))((.(((((....))))).))))))..)).)).))))....))--))...)..--)))....------------- ( -38.90)
>DroAna_CAF1 94924 100 + 1
UAAUUGGCAUGAACGCCACGGUCACCGGUUGGGGUCGCCUCAGCGAGGGCGGCACCCUGCCCUCGGUCCUCCAAGAGGUGAGUUCCAA------------------GUACUGGAUUAG
....((((......))))......(((((((((((((((((...((((((((....))))))))((....))..))))))).))))).------------------..)))))..... ( -44.20)
>DroPer_CAF1 79780 93 + 1
UAAUUGGCAUGAAUGCCACGGUCACCGGCUGGGGUCGUCUGAGCGAGGGCGGCACCCUGCCCUCGGUCCUCCAAGAGGUGAGUGCUUG---------G----------------UGGU
....(((((....)))))((.(((((...(((((......((.(((((((((....))))))))).)))))))...))))).))....---------.----------------.... ( -40.40)
>consensus
UAAUUGGCAUGAAUGCCACGGUCACCGGCUGGGGUCGUCUCAGCGAGGGCGGCACCCUGCCCUCGGUCCUCCAAGAGGUGAGUGCU____________________________U___
....((((......))))((.(((((.(((((((...)))))))((((((((....))))))))............))))).)).................................. (-33.80 = -34.47 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,969,837 – 11,969,955
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 73.23
Mean single sequence MFE -33.90
Consensus MFE -25.24
Energy contribution -25.63
Covariance contribution 0.39
Combinations/Pair 1.10
Mean z-score -0.88
Structure conservation index 0.74
SVM decision value 0.51
SVM RNA-class probability 0.765413
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11969837 118 - 27905053
UGAAUUCUAAAAAUGAAGCUUAAAGUCGUGUUAACACUCACCUCUUGGAGGACGGAGGGCAGGGUGCCGCCCUCGCUGAGACGACCCCAGCCGGUGACCGUGGCGUUCAUGCCAAUUA
..................(((...((((((....)))...((....))..))).)))(((((..((((((..((((((.(.(.......))))))))..))))))..).))))..... ( -36.00)
>DroVir_CAF1 85122 96 - 1
-------------UUGUGCU--AACU-------CCACUUACCUCCUGCAGCACCGAGGGCAGCGUACCGCCCUCGCUGAGGCGACCCCAGCCGGUGACCGUGGCAUUCAUGCCAAUCA
-------------(((.((.--....-------(((((((((.....((((...((((((........)))))))))).(((.......))))))))..)))).......)))))... ( -33.00)
>DroPse_CAF1 80411 93 - 1
ACCA----------------C---------CAAGCACUCACCUCUUGGAGGACCGAGGGCAGGGUGCCGCCCUCGCUCAGACGACCCCAGCCGGUGACCGUGGCAUUCAUGCCAAUUA
....----------------.---------.......(((((..((((.((..(((((((.((...))))))))).((....))))))))..)))))...(((((....))))).... ( -32.40)
>DroGri_CAF1 82817 101 - 1
-------------UUGAGAC--CAGUCGCA--UGCACUUACCUCCUGCAGCACCGACGGCAGCGUACCGCCCUCACUGAGACGACCCCAGCCGGUGACGGUGGCAUUCAUGCCAAUCA
-------------.(((...--..((((..--((((.........))))....))))((((..((.(((((.((((((.(.(.......)))))))).))))).))...))))..))) ( -31.40)
>DroAna_CAF1 94924 100 - 1
CUAAUCCAGUAC------------------UUGGAACUCACCUCUUGGAGGACCGAGGGCAGGGUGCCGCCCUCGCUGAGGCGACCCCAACCGGUGACCGUGGCGUUCAUGCCAAUUA
...........(------------------((((..(((........)))..)))))(((((..((((((..((((((.((.....))...))))))..))))))..).))))..... ( -38.20)
>DroPer_CAF1 79780 93 - 1
ACCA----------------C---------CAAGCACUCACCUCUUGGAGGACCGAGGGCAGGGUGCCGCCCUCGCUCAGACGACCCCAGCCGGUGACCGUGGCAUUCAUGCCAAUUA
....----------------.---------.......(((((..((((.((..(((((((.((...))))))))).((....))))))))..)))))...(((((....))))).... ( -32.40)
>consensus
___A____________________________AGCACUCACCUCUUGGAGGACCGAGGGCAGGGUGCCGCCCUCGCUGAGACGACCCCAGCCGGUGACCGUGGCAUUCAUGCCAAUUA
.....................................(((((............((((((........))))))((((.(.....).)))).)))))...(((((....))))).... (-25.24 = -25.63 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,969,917 – 11,970,014
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 93.20
Mean single sequence MFE -23.52
Consensus MFE -18.14
Energy contribution -18.62
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -1.62
Structure conservation index 0.77
SVM decision value 0.07
SVM RNA-class probability 0.570234
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11969917 97 - 27905053
CCAUUUAGAACCACACCGACAAUUUUUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGAAUUCUAAAAAUGAAGCUUAAAGUCGUGUUAACACU
...(((((((...((.((((((((..(((((.......)))))..).....))))))).))..)))))))................(((....))). ( -18.70)
>DroSec_CAF1 74194 97 - 1
CCAUUUAGAACCACACCGACAAUCUUUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGCAUUCUAAAAAUGAAGCUUAAAGUCGUGUUAACACU
...(((((((...((.(((((((((.(((((.......))))).)).....))))))).))..)))))))................(((....))). ( -20.30)
>DroSim_CAF1 74521 97 - 1
CCAUUUAGAACCACACCGACAAUCUUUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGCAUUCUAAAAAUGAACCUUAAAGUCGUGUUAACACU
...(((((((...((.(((((((((.(((((.......))))).)).....))))))).))..)))))))................(((....))). ( -20.30)
>DroEre_CAF1 74935 97 - 1
CCAUUAAGACCCACACCGACAAUCUGUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGGAUUCUAAAAAUGGAGCCUAAAGCUGUGUUAACACU
(((((.(((.(((...(((((((((((((((.......)))))))).....))))))).)))..)))...)))))(((.....)))(((....))). ( -27.90)
>DroYak_CAF1 77611 97 - 1
CCAAUAAGAACCACGCCGACAAUCUGUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGGAUUCUAAAAAUGGGCCUUAAAGCCGUGUUAACACU
......(((((((.((.((((((((((((((.......)))))))).....))))))))))).)))).......(((......)))(((....))). ( -30.40)
>consensus
CCAUUUAGAACCACACCGACAAUCUUUUGCGUUCGAUUCGCAGCGGUUAUCAUUGUCGCUGCAUUCUAAAAAUGAAGCUUAAAGUCGUGUUAACACU
...(((((((...((.(((((((((.(((((.......))))).)).....))))))).))..)))))))................(((....))). (-18.14 = -18.62 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:08 2006