Locus 8567

Sequence ID 3L_DroMel_CAF1
Location 22,350,218 – 22,350,356
Length 138
Max. P 0.999721
window14041 window14042 window14043

overview

Window 1

Location 22,350,218 – 22,350,316
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.92
Mean single sequence MFE -25.07
Consensus MFE -20.91
Energy contribution -20.47
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -2.67
Structure conservation index 0.83
SVM decision value 1.20
SVM RNA-class probability 0.930380
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22350218 98 - 23771897
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGGGAUGCCCUAC--CCCACU--------------------
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).)))))....((((((....))).))).....--......-------------------- ( -20.30)
>DroPse_CAF1 49851 115 - 1
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGAGACGCCC-----CCGACUGGCGGCGGCAGCGGCAGUGG
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).)))))....((((((....))).)))..-----((.((((.(.((....)).))))))) ( -32.40)
>DroSec_CAF1 1176 100 - 1
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGGGAUGCCCCACAACCCACU--------------------
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).)))))..............(((.((.....)).)))...-------------------- ( -21.50)
>DroSim_CAF1 14593 100 - 1
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUAAAUUUGCAUUUAAUUUGCGCUUACGAGGGAUGCCCCACAACCCACU--------------------
...........((..(((((((((((((((((.....)))))).)))))))))))....(((.......)))......))(((.((.....)).)))...-------------------- ( -20.10)
>DroEre_CAF1 18020 98 - 1
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGGGACGCCGCCC--CCUACU--------------------
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).)))))....((((((....))).))).....--......-------------------- ( -22.20)
>DroPer_CAF1 52410 115 - 1
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGAGACGCCC-----CCGACUGGCGGAGGCAGCGGCAGAGG
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).))))).((((((((..(....)..(((.-----(((.....))).)))))).))))).. ( -33.90)
>consensus
UAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGAGGGACGCCCCAC__CCCACU____________________
(((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).)))))....((((((....))).)))................................. (-20.91 = -20.47 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,350,236 – 22,350,356
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -28.63
Consensus MFE -25.64
Energy contribution -25.67
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -3.14
Structure conservation index 0.90
SVM decision value 3.68
SVM RNA-class probability 0.999517
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22350236 120 + 23771897
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCACUUUAACGCUGAAGAGCUCGGCUUCACCA
.(....).(((.......)))..((((((((((((..((((((.....)))))).....))))))))))))(((((..(((((((....)))))))..(((((.....)))))))))).. ( -31.60)
>DroPse_CAF1 49886 120 + 1
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCCAGUCCCAGU
..(.(((((((.......)))..((((((((((((..((((((.....)))))).....)))))))))))).....(((..((((............))))..))))))))......... ( -26.90)
>DroSec_CAF1 1196 120 + 1
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCGGCUCCACCA
..(..(((((...(((.((.((.((((((((((((..((((((.....)))))).....)))))))))))).)).)).))).)))))..)........(((((.....)))))....... ( -29.90)
>DroSim_CAF1 14613 120 + 1
UCGUAAGCGCAAAUUAAAUGCAAAUUUAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCGGCUCCACCA
..(.((((((...(((.((.((.((((((((((((..((((((.....)))))).....)))))))))))).)).)).))).)))))).)........(((((.....)))))....... ( -26.60)
>DroEre_CAF1 18038 120 + 1
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCGGCUCCACCA
..(..(((((...(((.((.((.((((((((((((..((((((.....)))))).....)))))))))))).)).)).))).)))))..)........(((((.....)))))....... ( -29.90)
>DroPer_CAF1 52445 120 + 1
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCCAGUCCNNNN
..(.(((((((.......)))..((((((((((((..((((((.....)))))).....)))))))))))).....(((..((((............))))..))))))))......... ( -26.90)
>consensus
UCGUGAGCGCAAAUUAAAUGCAAAUUCAAUUAAUUUGAAGCAAACAAUUUGCUUAAAUUAAUUAAUUGAAUGUGAAUCUAAAGUGCUUCCAAUUUAACGCUGAAGAGCUCGGCUCCACCA
....(((((((.......)))..((((((((((((..((((((.....)))))).....)))))))))))).....(((..((((............))))..))))))).......... (-25.64 = -25.67 +   0.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,350,236 – 22,350,356
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -31.38
Consensus MFE -28.41
Energy contribution -28.60
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -3.16
Structure conservation index 0.91
SVM decision value 3.95
SVM RNA-class probability 0.999721
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22350236 120 - 23771897
UGGUGAAGCCGAGCUCUUCAGCGUUAAAGUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
.((.....))((((..(((.((......)).)))(((..((((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).))))))..))))))).... ( -33.40)
>DroPse_CAF1 49886 120 - 1
ACUGGGACUGGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
..........((((..(((((.......))))).(((..((((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).))))))..))))))).... ( -29.70)
>DroSec_CAF1 1196 120 - 1
UGGUGGAGCCGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
..(((((((...))))...(((((.((((((((.(((.....((.......))..(((((((((((((((((.....)))))).)))))))))))...))).)))))))))))))))).. ( -32.30)
>DroSim_CAF1 14613 120 - 1
UGGUGGAGCCGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUAAAUUUGCAUUUAAUUUGCGCUUACGA
..(.(((((...))))).)(((((.((((((((.(((.....((.......))..(((((((((((((((((.....)))))).)))))))))))...))).)))))))))))))..... ( -30.90)
>DroEre_CAF1 18038 120 - 1
UGGUGGAGCCGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
..(((((((...))))...(((((.((((((((.(((.....((.......))..(((((((((((((((((.....)))))).)))))))))))...))).)))))))))))))))).. ( -32.30)
>DroPer_CAF1 52445 120 - 1
NNNNGGACUGGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
..........((((..(((((.......))))).(((..((((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).))))))..))))))).... ( -29.70)
>consensus
UGGUGGAGCCGAGCUCUUCAGCGUUAAAUUGGAAGCACUUUAGAUUCACAUUCAAUUAAUUAAUUUAAGCAAAUUGUUUGCUUCAAAUUAAUUGAAUUUGCAUUUAAUUUGCGCUCACGA
..........((((..(((((.......))))).(((..((((((.((.((((((((((((.....((((((.....))))))..)))))))))))).)).))))))..))))))).... (-28.41 = -28.60 +   0.19)

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 13:19:15 2006