Locus 4188

Sequence ID 3R_DroMel_CAF1
Location 11,343,224 – 11,343,454
Length 230
Max. P 0.995654
window6735 window6736 window6737 window6738

overview

Window 5

Location 11,343,224 – 11,343,344
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -28.71
Consensus MFE -26.04
Energy contribution -25.88
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.18
Structure conservation index 0.91
SVM decision value -0.05
SVM RNA-class probability 0.506918
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11343224 120 - 27905053
UGCGGAUUAACUUUUUACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAUAUUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCACAC
.((((....((.................((....))....((((((..(((......))).........((((((.(..........).))))))....))))))))...))))...... ( -26.40)
>DroSec_CAF1 82075 120 - 1
UGCGGAUUAACUUUUAACCAAUUUAGAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAUAUUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCACAC
...((.(((.....)))))......((((((...((....((((((..(((......))).........((((((.(..........).))))))....)))))).))..)))))).... ( -28.20)
>DroSim_CAF1 80633 120 - 1
UGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAUAUUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCACAC
.((((....((.................((....))....((((((..(((......))).........((((((.(..........).))))))....))))))))...))))...... ( -26.40)
>DroEre_CAF1 78371 120 - 1
UGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUGCCCCACACUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCCCAC
.((((............(((........)))..(((....((((((..(((((.((((......)))).))..)))..((((.....))))........)))))).))).))))...... ( -32.20)
>DroYak_CAF1 80403 120 - 1
UGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACUCCAUACUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCACAC
.((((............(((........)))..(((....((((((..(((......))).........((((((..............))))))....)))))).))).))))...... ( -30.34)
>consensus
UGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAUAUUGAAAGUGUAAUAAAAAGCAGCUGUGCGCCGCUCACAC
.((((....((......(((........))).........((((((..(((......))).........((((((..............))))))....))))))))...))))...... (-26.04 = -25.88 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,343,264 – 11,343,384
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -32.21
Consensus MFE -31.34
Energy contribution -31.54
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.97
SVM decision value 2.60
SVM RNA-class probability 0.995654
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11343264 120 - 27905053
GGCCUAUACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUUACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAU
(((....((((((.....)))))).(((((.(......(((((((......(((((((.........)))))))........)))))))....).))))))))................. ( -30.64)
>DroSec_CAF1 82115 120 - 1
GGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUAGAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAU
(((...(((((((.....)))))))(((((.(......(((((((....(((((..........)))))(....).......)))))))....).))))))))................. ( -33.90)
>DroSim_CAF1 80673 120 - 1
GGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAU
(((...(((((((.....)))))))(((((.(......(((((((............(((........)))...........)))))))....).))))))))................. ( -32.00)
>DroEre_CAF1 78411 120 - 1
GGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUGCCCCAC
(((...(((((((.....)))))))(((...........((((..............(((........))).(((......)))))))(((......))))))..........))).... ( -32.40)
>DroYak_CAF1 80443 120 - 1
GGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACUCCAU
(((...(((((((.....)))))))(((((.(......(((((..............(((........))).(((......))))))))....).))))))))................. ( -32.10)
>consensus
GGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACAAGCUGCAAGGCCAAGAUGCCGCCAUAUCCUGUUACCCCAU
(((...(((((((.....)))))))(((((.(......(((((((............(((........)))...........)))))))....).))))))))................. (-31.34 = -31.54 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,343,304 – 11,343,414
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.65
Mean single sequence MFE -28.80
Consensus MFE -21.10
Energy contribution -21.70
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.73
SVM decision value 0.97
SVM RNA-class probability 0.892871
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11343304 110 - 27905053
ACGCGUGUC----AGCUCACGCACACUACUG------CACGGCCUAUACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUUACCAAUUUACAGUGGAAACAAACA
..(((((..----....)))))...((((((------.((((((...((((((.....)))))).))).)))..((((((.(..((.......))..).))))))))))))......... ( -33.10)
>DroSec_CAF1 82155 114 - 1
ACGCGUGUCAGUCAGCUCUCGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUAGAGUGGAAACAAACA
.((((((.((((..((....)).....))))------))).(((..(((((((.....)))))))))).............))).....................(..((....))..). ( -30.40)
>DroSim_CAF1 80713 114 - 1
ACGCGUGUCAGUCAGCUCACGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACA
..(((((..((....)))))))...((((((------.((((((..(((((((.....)))))))))).)))...........((.(((.....)))))......))))))......... ( -31.30)
>DroEre_CAF1 78451 97 - 1
-----------------CACGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACA
-----------------...((...((((((------.((((((..(((((((.....)))))))))).)))...........((.(((.....)))))......))))))..))..... ( -25.30)
>DroYak_CAF1 80483 103 - 1
-----------------CACGCACACUACUACGCACACACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAGCAAACA
-----------------...((...(((((..(((...((((((..(((((((.....)))))))))).)))........)))((.(((.....))))).......)))))..))..... ( -23.90)
>consensus
ACGCGUGUC____AGCUCACGCACACUACUG______CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUUUGCGGAUUAACUUUUAACCAAUUUACAGUGGAAACAAACA
.........................((((((.......((((((..(((((((.....)))))))))).)))..((((((.(..((.......))..).))))))))))))......... (-21.10 = -21.70 +   0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,343,344 – 11,343,454
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.80
Mean single sequence MFE -34.54
Consensus MFE -25.72
Energy contribution -25.72
Covariance contribution 0.00
Combinations/Pair 1.10
Mean z-score -2.63
Structure conservation index 0.74
SVM decision value 2.52
SVM RNA-class probability 0.994866
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11343344 110 - 27905053
AUGGCGGGAAAAUGAAAAGAGGCGGGAAAGCCUAACGCACACGCGUGUC----AGCUCACGCACACUACUG------CACGGCCUAUACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
((((((((....(((....((((......)))).((((....)))).))----).)))..(((......))------)...(((...((((((.....)))))).)))..)))))..... ( -36.90)
>DroSec_CAF1 82195 114 - 1
AUGGCGGGGAAAUGAGAAGAGGCGGGAAAGCCUAAUACACACGCGUGUCAGUCAGCUCUCGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
((((((((((..(((....((((......))))...((((....))))...)))..))))(((......))------)...(((..(((((((.....)))))))))).))))))..... ( -37.50)
>DroSim_CAF1 80753 114 - 1
AUGGCGGGGAAAUGAAAAGAGGCGGGAAAGCCUAAUACACACGCGUGUCAGUCAGCUCACGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
((((((.((..........((((......)))).........(((((..((....)))))))......)).------)...(((..(((((((.....))))))))))..)))))..... ( -36.00)
>DroEre_CAF1 78491 89 - 1
GUGGCAGGAAAAUCAAAAG-GGCGAGAGAGCCU------------------------CACGCACACUACUG------CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
((((((............(-(((......))))------------------------...(((......))------)...(((..(((((((.....)))))))))).))))))..... ( -28.90)
>DroYak_CAF1 80523 96 - 1
AUGGCAGUGAAAUCAAACGAGGCCAGAAUGCCU------------------------CACGCACACUACUACGCACACACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
(((((((((.........(((((......))))------------------------)..((..........)).)))...(((..(((((((.....)))))))))).))))))..... ( -33.40)
>consensus
AUGGCGGGGAAAUGAAAAGAGGCGGGAAAGCCUAA__CACACGCGUGUC____AGCUCACGCACACUACUG______CACGGCCUAGACAGCCAAAAUGGCUGUUGGCAUGUCAUAAAUU
((((((.............((((......))))................................................(((..(((((((.....)))))))))).))))))..... (-25.72 = -25.72 +   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 11:20:54 2006