Locus 884

Sequence ID 2R_DroMel_CAF1
Location 4,036,295 – 4,036,455
Length 160
Max. P 0.996622
window1542 window1543 window1544 window1545

overview

Window 2

Location 4,036,295 – 4,036,415
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.64
Mean single sequence MFE -30.74
Consensus MFE -26.19
Energy contribution -26.43
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.85
SVM decision value 1.23
SVM RNA-class probability 0.933868
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036295 120 + 20766785
GCCUCUUUAGACCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUAAACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
((.....((((..((((.....((((((((((((....)))))......(((.....)))....)))))))...))))))))(((((((....))))).)).......)).......... ( -27.00)
>DroSec_CAF1 18960 119 + 1
GCAUCUUUAUGCCAAGUAUUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCAUGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
((((..((.(((((..(((((...((((((((((....))))).....-)))))..)))))(((((((.(........).))))))).........)).)))))..)))).......... ( -27.60)
>DroSim_CAF1 21091 119 + 1
GCAUCUUUGGGCCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUUA
....(((((((((((((.....((((((((((((....))))).....-(((.....)))....)))))))...)))...)))))..............(((.....))).))))).... ( -32.70)
>DroEre_CAF1 18089 118 + 1
GCCUCUUUAGGCCAAGUCCUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGU-UCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
.........(((((.(..((..((((((((((((....))))).....-(((.....)))....)))))))...)).-.)))))).(((..((((.((((.......)))).)))).))) ( -32.20)
>DroYak_CAF1 22183 119 + 1
GCCUCUUUGGGCCAAGUCCUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
....((((((((((.(..((..((((((((((((....))))).....-(((.....)))....)))))))...))..).)))))..............(((.....))).))))).... ( -34.20)
>consensus
GCCUCUUUAGGCCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUA_ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
.........(((((........((((((((((((....)))))......(((.....)))....))))))).........)))))...........((.(((.....))).))....... (-26.19 = -26.43 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 3

Location 4,036,295 – 4,036,415
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.64
Mean single sequence MFE -32.00
Consensus MFE -28.79
Energy contribution -29.03
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.06
Structure conservation index 0.90
SVM decision value 2.72
SVM RNA-class probability 0.996622
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036295 120 - 20766785
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGUUUAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGUCUAAAGAGGC
....(((((((((.....)))))............((((((...(.....)(((((((((.....)))))......((((((....)))))))))).........))))))...)))).. ( -29.40)
>DroSec_CAF1 18960 119 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACAUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAAUACUUGGCAUAAAGAUGC
....(((((((((.....))))).............((((...(((((...(((((((((.....))))))-))).((((((....)))))).........)))))))))..)))).... ( -31.00)
>DroSim_CAF1 21091 119 - 1
UAAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGCCCAAAGAUGC
....(((((((((.....)))))............((((((..........(((((((((.....))))))-))).((((((....)))))).............)))))).)))).... ( -31.80)
>DroEre_CAF1 18089 118 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGA-ACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAGGACUUGGCCUAAAGAGGC
....(((((((((.....)))))............((((((.-.((.....(((((((((.....))))).-....((((((....)))))))))).....))..))))))...)))).. ( -34.10)
>DroYak_CAF1 22183 119 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAGGACUUGGCCCAAAGAGGC
....(((((((((.....)))))............((((((...((.....(((((((((.....))))).-....((((((....))))))))))....))...))))))...)))).. ( -33.70)
>consensus
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU_UAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGCCUAAAGAGGC
....(((((((((.....)))))............((((((..........(((((((((.....)))))......((((((....)))))))))).........)))))).)))).... (-28.79 = -29.03 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 4

Location 4,036,335 – 4,036,455
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.49
Mean single sequence MFE -31.44
Consensus MFE -30.36
Energy contribution -30.20
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.20
Structure conservation index 0.97
SVM decision value 0.38
SVM RNA-class probability 0.714400
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036335 120 + 20766785
UGCAGAUAAACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGUAAAAUUCAA
.((((.....((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -30.90)
>DroSec_CAF1 19000 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCAUGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((...-.((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -31.60)
>DroSim_CAF1 21131 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUUAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
........-.((.(((((.(((((((((.(........).))))))).........((.(((.....))).)).....)).)))))((((.(.(((.....))))))))))......... ( -31.10)
>DroEre_CAF1 18129 117 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGU-UCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGA-AAUUCAA
.((((...-.((.(((.(((.(((((((.(.......-.)))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))....-....... ( -32.00)
>DroYak_CAF1 22223 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((...-.((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -31.60)
>consensus
UGCAGAUA_ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((.....((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ (-30.36 = -30.20 +  -0.16) 

alignment

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secondary structure

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dotplot

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Window 5

Location 4,036,335 – 4,036,455
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.49
Mean single sequence MFE -32.16
Consensus MFE -31.38
Energy contribution -31.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.98
SVM decision value 1.31
SVM RNA-class probability 0.940562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036335 120 - 20766785
UUGAAUUUUACCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGUUUAUCUGCA
...........((((((((.....))))..))))..(((.((((((.((((((.....)))))).........(((((((............))))))).........)))))).))).. ( -32.00)
>DroSec_CAF1 19000 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACAUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -32.80)
>DroSim_CAF1 21131 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUAAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -31.90)
>DroEre_CAF1 18129 117 - 1
UUGAAUU-UCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGA-ACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
.......-....((((.((..(((((((...((.....)).......((((((.....)))))).........((((((((.-.......).))))))).))))))).)).-...)))). ( -32.20)
>DroYak_CAF1 22223 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -31.90)
>consensus
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU_UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).....)))). (-31.38 = -31.38 +   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 09:50:04 2006