Locus 7466

Sequence ID 3R_DroMel_CAF1
Location 19,938,666 – 19,938,801
Length 135
Max. P 0.997509
window12069 window12070 window12071 window12072

overview

Window 9

Location 19,938,666 – 19,938,762
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -35.62
Consensus MFE -32.16
Energy contribution -31.80
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.29
Structure conservation index 0.90
SVM decision value 0.54
SVM RNA-class probability 0.773210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19938666 96 + 27905053
UUGACAGCAGGUUCUCUCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
..........((((((((.(((.....((((....))))...)))((((((.......))))))......))))))))(((((.......))))). ( -37.90)
>DroSec_CAF1 3565 96 + 1
CUGGCAGCAAGUUUCCUCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
(((((.((.....(((((.(((.....))).))).))......)))))))............((((((....))))))(((((.......))))). ( -38.30)
>DroSim_CAF1 3577 96 + 1
CUGACAGUGAGUUUCCUCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
..(((..((((....))))((..((....))..)).)))....((((((((.......))))))((((....))))))(((((.......))))). ( -33.50)
>DroEre_CAF1 3623 96 + 1
UUGACAACGAGUUCCCCCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
..(((.....((((..(((((...)))))..)))).)))....((((((((.......))))))((((....))))))(((((.......))))). ( -34.10)
>DroYak_CAF1 3630 96 + 1
UUGACAACAAGUUCCCUCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
.........((..(((((.(((.....))).))).)).))...((((((((.......))))))((((....))))))(((((.......))))). ( -34.30)
>consensus
UUGACAGCAAGUUCCCUCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACA
.........((..(((((.(((.....))).))).)).))...((((((((.......))))))((((....))))))(((((.......))))). (-32.16 = -31.80 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,938,666 – 19,938,762
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -34.38
Consensus MFE -31.94
Energy contribution -31.78
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.56
Structure conservation index 0.93
SVM decision value 1.69
SVM RNA-class probability 0.972371
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19938666 96 - 27905053
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGAGAGAACCUGCUGUCAA
.(((((.......)))))((((((....)))).(((((.......))))).))....(((..(((((((.....)))))))((......))))).. ( -33.10)
>DroSec_CAF1 3565 96 - 1
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGAGGAAACUUGCUGCCAG
.(((((.......)))))(((((.((....))...)))))......(((((((...((....(((((((.....)))))))....)).)).))))) ( -36.00)
>DroSim_CAF1 3577 96 - 1
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGAGGAAACUCACUGUCAG
.(((((.......)))))((((((....)))).(((((.......))))).))....(((.....((((.....))))(((....)))...))).. ( -33.80)
>DroEre_CAF1 3623 96 - 1
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGGGGGAACUCGUUGUCAA
.(((((.......))))).........((((..(((((.......))))).........((.(((((((.....)))))))))..))))....... ( -34.10)
>DroYak_CAF1 3630 96 - 1
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGAGGGAACUUGUUGUCAA
.(((((.......)))))((((((....)))).(((((.......))))).))......((.(((((((.....)))))))))............. ( -34.90)
>consensus
UGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGAGGGAACUUGCUGUCAA
.(((((.......)))))((((((....)))).(((((.......))))).)).........(((((((.....)))))))............... (-31.94 = -31.78 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,938,682 – 19,938,801
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 90.30
Mean single sequence MFE -42.95
Consensus MFE -41.20
Energy contribution -41.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.96
SVM decision value 2.87
SVM RNA-class probability 0.997509
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19938682 119 + 27905053
UCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAGUAAAAUUUGUUUUUUUUUUUAGAAUGAC
((((((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))(((((.((((.....)))).)))))....))). ( -42.00)
>DroSec_CAF1 3581 116 + 1
UCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAUGAGUGAAAUUUCUUUU---CUUUAGAAUGAC
((((((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......)))))))))))).)))..((((.....)))---)........... ( -43.30)
>DroSim_CAF1 3593 115 + 1
UCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAGAGGAAAAUUUGUUUU----UUUAGAAUAAC
...(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))...(((((((....))))----)))........ ( -41.90)
>DroYak_CAF1 3646 112 + 1
UCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAAGAAAGUUUGUUUUUUUUUU-------UU
...(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))((((((((((......))))))))-------)) ( -44.60)
>consensus
UCAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAGGAAAAUUUGUUUU___UUUUAGAAUGAC
...(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))................................. (-41.20 = -41.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,938,682 – 19,938,801
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 90.30
Mean single sequence MFE -36.17
Consensus MFE -35.00
Energy contribution -35.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.97
SVM decision value 2.38
SVM RNA-class probability 0.993251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19938682 119 - 27905053
GUCAUUCUAAAAAAAAAAACAAAUUUUACUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGA
.....(((((...((((......))))......((((((((((((.......)))))(((((.((....))...)))))....)))))))...)))))....((((((.....)))))) ( -35.60)
>DroSec_CAF1 3581 116 - 1
GUCAUUCUAAAG---AAAAGAAAUUUCACUCAUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGA
.....(((((.(---(((.....))))......((((((((((((.......)))))(((((.((....))...)))))....)))))))...)))))....((((((.....)))))) ( -38.30)
>DroSim_CAF1 3593 115 - 1
GUUAUUCUAAA----AAAACAAAUUUUCCUCUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGA
...........----..................((((((((((((.......)))))(((((.((....))...)))))....)))))))((........))((((((.....)))))) ( -35.00)
>DroYak_CAF1 3646 112 - 1
AA-------AAAAAAAAAACAAACUUUCUUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGA
..-------.................(((...(((((((((((((.......)))))(((((.((....))...)))))....))))))))....)))....((((((.....)))))) ( -35.80)
>consensus
GUCAUUCUAAAA___AAAACAAAUUUUACUCUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGA
.................................((((((((((((.......)))))(((((.((....))...)))))....)))))))((........))((((((.....)))))) (-35.00 = -35.00 +   0.00)

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 12:46:46 2006