Locus 2814

Sequence ID 2R_DroMel_CAF1
Location 9,806,313 – 9,806,544
Length 231
Max. P 0.801027
window4651 window4652 window4653 window4654

overview

Window 1

Location 9,806,313 – 9,806,433
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -32.59
Consensus MFE -28.99
Energy contribution -29.27
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -1.14
Structure conservation index 0.89
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9806313 120 + 20766785
GUCGUUGUACGGCACUCCGAAAGAGGAGCCCAUGCCCAACAUACCGAUCGUGUCGGAAAAAGUCUCUGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACGGACAACCG
...(((((.((((....(....).((((((.(((.........(((((...)))))..........(((.((((..((....))..)))))))..))))))))).))))....))))).. ( -32.50)
>DroVir_CAF1 48020 120 + 1
GUCGUUGUACGGCACUCCGAAAGAGGAGCCAAUGCCCAAUAUACCGAUAGUCUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCG
(((..(((.((((....(....).(((((((............((((.....))))...........((.((((..((....))..)))))).....))))))).))))))))))..... ( -32.20)
>DroPse_CAF1 42898 120 + 1
GUCGUUGUACGGCACUCCGAAAGAGGAGCCGAUGCCGAACAUACCGAUCGUGUCGGAAAAAGUCUCUGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACGGACAAUCG
(((..(((.((((....(....).(((((((((.((((.(((.......))))))).....)))..(((.((((..((....))..))))))).....)))))).))))))))))..... ( -34.10)
>DroGri_CAF1 53063 120 + 1
GUCGUUGUACGGCACUCCGAAAGAGGAGCCAAUGCCCAACAUACCAAUAGUCUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCG
(((..(((.((((....(....).((((((((((.....)))..((((.(.((.(((((..((....))...))))).....)).).))))......))))))).))))))))))..... ( -30.60)
>DroWil_CAF1 53166 120 + 1
GUCGUUGUACGGCACUCCGAAAGAGGAGCCCAUGCCCAAUAUACCUAUCGUGUCCGAGAAGGUCUCUGCUAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCG
(((..(((.((((....(....).((((((.(((........((((.(((....)))..))))...(((.((((..((....))..)))))))..))))))))).))))))))))..... ( -33.00)
>DroMoj_CAF1 58570 120 + 1
GUCGUUGUACGGCACUCCGAAAGAGGAGCCAAUGCCCAAUAUACCGAUAGUAUCGGAAAAAGUCUCGGCCAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCG
(((..(((.((((....(....).(((((((..(((.......(((((...)))))..........)))(((((..((....))..)))))......))))))).))))))))))..... ( -33.13)
>consensus
GUCGUUGUACGGCACUCCGAAAGAGGAGCCAAUGCCCAACAUACCGAUAGUGUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCG
(((..(((.((((....(....).((((((.(((.........((((.....))))...........((.((((..((....))..))))))...))))))))).))))))))))..... (-28.99 = -29.27 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,806,353 – 9,806,473
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -36.35
Consensus MFE -30.35
Energy contribution -31.10
Covariance contribution 0.75
Combinations/Pair 1.06
Mean z-score -2.11
Structure conservation index 0.83
SVM decision value 0.62
SVM RNA-class probability 0.801027
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9806353 120 + 20766785
AUACCGAUCGUGUCGGAAAAAGUCUCUGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACGGACAACCGACUGGCCAUGAAACUGUUUGGCAGCCGAAAGGCGCUGGUC
.....((((.(((((((...(((...(((.((((..((....))..))))))).((((((..((((....(((....))).)))))))))).))).)))))))(((....)))...)))) ( -35.80)
>DroVir_CAF1 48060 120 + 1
AUACCGAUAGUCUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCCUUGGUC
..(((((.......(((((..((....))...)))))......(((((......((((((..((((.(((.......))).))))))))))......))))).(((....))).))))). ( -36.00)
>DroGri_CAF1 53103 120 + 1
AUACCAAUAGUCUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGGAAGGCUUUGGUC
..(((((.......(((((..((....))...)))))......(((((......((((((..((((.(((.......))).))))))))))......)))))((((....))))))))). ( -37.40)
>DroWil_CAF1 53206 120 + 1
AUACCUAUCGUGUCCGAGAAGGUCUCUGCUAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCAUUGGUC
..((((.(((....)))..))))....((((((..........(((((......((((((..((((.(((.......))).))))))))))......))))).(((....))))))))). ( -35.80)
>DroMoj_CAF1 58610 120 + 1
AUACCGAUAGUAUCGGAAAAAGUCUCGGCCAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCCUUGGUC
...(((((...)))))..........((((((...........(((((......((((((..((((.(((.......))).))))))))))......))))).(((....))).)))))) ( -37.90)
>DroAna_CAF1 44832 120 + 1
AUACCGAUCGUGUCGGAAAAAGUCUCUGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCAACGGACAACCGACUGGCCAUGAAACUGUUUGGCAGCCGAAAGGCACUCGUC
...(((((...)))))...........((((............(((((..(((.((((((..((((....(((....))).))))))))))...)))))))).(((....)))..)))). ( -35.20)
>consensus
AUACCGAUAGUGUCGGAAAAAGUCUCGGCGAAUUUCCUAAAAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCAUUGGUC
..((((........(((((..((....))...)))))......(((((......((((((..((((.(((.......))).))))))))))......))))).(((....)))..)))). (-30.35 = -31.10 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,806,393 – 9,806,513
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.61
Mean single sequence MFE -35.30
Consensus MFE -31.82
Energy contribution -31.77
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.15
Structure conservation index 0.90
SVM decision value 0.08
SVM RNA-class probability 0.573841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9806393 120 + 20766785
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACGGACAACCGACUGGCCAUGAAACUGUUUGGCAGCCGAAAGGCGCUGGUCAAGGAGCGCAUACGUCAGAAAACUUCCGGGCACUGGGUCA
...(((...(((..((((((..((((....(((....))).))))))))))..((.((((((.(((....)))....)))))).)).)))..((..((....))..)))))......... ( -37.50)
>DroVir_CAF1 48100 120 + 1
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCCUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUAA
...(((...(((..((((((..((((.(((.......))).)))))))))).....((((((.(((....)))....))))))....)))..((..((....))..)))))......... ( -34.60)
>DroGri_CAF1 53143 120 + 1
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGGAAGGCUUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUUA
.((.(((((.((....(((((((..((((((((((....)))))((((..........))))((((....)))))))))....)))).))).((..((....))..)).))))))).)). ( -35.70)
>DroMoj_CAF1 58650 120 + 1
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCCUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUAA
...(((...(((..((((((..((((.(((.......))).)))))))))).....((((((.(((....)))....))))))....)))..((..((....))..)))))......... ( -34.60)
>DroAna_CAF1 44872 120 + 1
AAAGUCAAUUGCAAUCAUGGUUCCAGCCAACGGACAACCGACUGGCCAUGAAACUGUUUGGCAGCCGAAAGGCACUCGUCAAGGAGCGAAUACGUCAGAAAACUUCCGGGCAUUGGGUCA
....(((((.((..((((((..((((....(((....))).)))))))))).....((((((.(((....)))..((((......))))....))))))..........))))))).... ( -35.70)
>DroPer_CAF1 42943 120 + 1
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACGGACAAUCGUUUGGCCAUGAAACUAUUUGGCAGCCGCAAGGCAUUGGUCAAGGAGCGCAUACGUCAGAAAACUUCCGGUCAUUGGGUCA
....(((((.((....((((((((.((((((((((....)))))((((..........)))).(((....))).)))))...))))).))).((..((....))..)))).))))).... ( -33.70)
>consensus
AAAGUCAAUUGCAAUCAUGGUUCCAGCCGACAGACAAUCGUCUGGCCAUGAAACUAUUUGGCAGCCGCAAGGCAUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUCA
...(((...(((..((((((..((((.(((.......))).))))))))))..((.((((((.(((....)))....)))))).)).)))..((..((....))..)))))......... (-31.82 = -31.77 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,806,433 – 9,806,544
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.17
Mean single sequence MFE -35.83
Consensus MFE -33.21
Energy contribution -32.90
Covariance contribution -0.31
Combinations/Pair 1.06
Mean z-score -1.45
Structure conservation index 0.93
SVM decision value 0.59
SVM RNA-class probability 0.793464
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9806433 111 + 20766785
ACUGGCCAUGAAACUGUUUGGCAGCCGAAAGGCGCUGGUCAAGGAGCGCAUACGUCAGAAAACUUCCGGGCACUGGGUCAUACACCCGUGCAGUUCAUUCAGGUGAG------UUCC---
(((.(((.((((.((..(..((.(((....)))))..)...))((((.....((..((....))..)).((((.((((.....)))))))).)))).))))))).))------)...--- ( -40.30)
>DroVir_CAF1 48140 111 + 1
UCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCCUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUAAUACACCCGUGCAGUUCAUUCAGGUAUG------CCAC---
..((((..((((....((((((.(((....)))....))))))((((((((..(((.(........).)))...((((.....)))))))).)))).)))).....)------))).--- ( -35.10)
>DroPse_CAF1 43018 114 + 1
UUUGGCCAUGAAACUAUUUGGCAGCCGCAAGGCAUUGGUCAAGGAGCGCAUACGUCAGAAAACUUCCGGUCAUUGGGUCAUACACCCGUGCAGUUCAUUCAGGUGAG------UUGUGCU
..(((((..........(((((.(((....)))....)))))((((((....))).........))))))))..((((.....))))(..((..((((....)))).------.))..). ( -35.40)
>DroGri_CAF1 53183 117 + 1
UCUGGCCAUGAAAUUAUUUGGCAGCCGGAAGGCUUUGGUCAAAGAACGCAUACGUCAGAAAACUUCCGGGCAUUGGGUUAUACACCCGUGCAGUUCAUUCAGGUAAUUGAAACCCAC---
((((((.(((......((((((((((....))))...)))))).....)))..))))))........((((((.((((.....))))))))......(((((....)))))..))..--- ( -35.80)
>DroWil_CAF1 53286 108 + 1
UCUGGCCAUGAAAUUAUUUGGCAGCCGCAAGGCAUUGGUCAAAGAGCGCAUACGUCAGAAAACUUCCGGGCAUUGGGUAAUACACCCUUGCAGUUCAUUCAGGUAUU------U------
....(((.((((....((((((.(((....)))....))))))((((.....((..((....))..)).(((..((((.....)))).))).)))).)))))))...------.------ ( -33.00)
>DroPer_CAF1 42983 114 + 1
UUUGGCCAUGAAACUAUUUGGCAGCCGCAAGGCAUUGGUCAAGGAGCGCAUACGUCAGAAAACUUCCGGUCAUUGGGUCAUACACCCGUGCAGUUCAUUCAGGUGAG------UUGUGCU
..(((((..........(((((.(((....)))....)))))((((((....))).........))))))))..((((.....))))(..((..((((....)))).------.))..). ( -35.40)
>consensus
UCUGGCCAUGAAACUAUUUGGCAGCCGCAAGGCAUUGGUCAAAGAGCGCAUACGUCAGAAAACUUCCGGGCAUUGGGUCAUACACCCGUGCAGUUCAUUCAGGUAAG______UUAC___
....(((.((((....((((((.(((....)))....))))))((((((((.((..((....))..))......((((.....)))))))).)))).)))))))................ (-33.21 = -32.90 +  -0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:07 2006