Locus 2415

Sequence ID 3R_DroMel_CAF1
Location 6,760,588 – 6,760,726
Length 138
Max. P 0.997659
window3926 window3927 window3928

overview

Window 6

Location 6,760,588 – 6,760,686
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.34
Mean single sequence MFE -49.30
Consensus MFE -35.12
Energy contribution -35.40
Covariance contribution 0.28
Combinations/Pair 1.17
Mean z-score -3.96
Structure conservation index 0.71
SVM decision value 2.90
SVM RNA-class probability 0.997659
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6760588 98 + 27905053
GACAGCCGGGUCUUGAAGUCUCAGAGUUUCUGAGUCUUGGGGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUCCUAGUCGGG-GGAACUGGCCCCCGGUU
...(((((((.(((.(((.(((((.....))))).))).))).)))---------------------(((((((..(((((.....))))).)))))))(((-((......))))))))) ( -48.60)
>DroSec_CAF1 24831 98 + 1
GACAGCCGGGUCUUGAAGUCUCAGAGUCUUUGAGUCUUGGGGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG-GGAACUGGCCCCCGGUU
...(((((((.(((.(((.((((((...)))))).))).))).)))---------------------(((((((..(((((.....))))).)))))))(((-((......))))))))) ( -43.10)
>DroSim_CAF1 29205 98 + 1
GACAGCCGGGUCUUGAAGUCUCAGAGUCUCUGAGUCUUGGGGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG-GGAACUGGCCCCCGGUU
...(((((((.(((.(((.(((((.....))))).))).))).)))---------------------(((((((..(((((.....))))).)))))))(((-((......))))))))) ( -46.00)
>DroEre_CAF1 9291 106 + 1
GACAGCCGGGUCUUGAAGUCUCAGAGUCUCUGAGUCCUGGGGUCUCGGG--------------GCCCGGCUGGGUUGUCAACUUAUUUGAGUUCCAGUCGGGGGGAACUGGCCCCCGGUU
..((((((((((((((..((((((.(.(.....).)))))))..)))))--------------)))))))))((...((((.....))))...))(..((((((.......))))))..) ( -53.50)
>DroYak_CAF1 21385 120 + 1
GACAGCCGGGUCUUGAAGUCUCAGAGUAUCUUAGUCCUGGGGUCUCGGGACUCGGUACUCGGGACUCGGCUGGGUUGUCAACUUAUUUGACUCCUGGCGAGGGGAAAGUGGCCCCCGGUU
..((((((((((((((....)).(((((((..((((((((....)))))))).)))))))))))))))))))((..(((((.....))))).))...((.((((.......))))))... ( -55.30)
>consensus
GACAGCCGGGUCUUGAAGUCUCAGAGUCUCUGAGUCUUGGGGUCUC_____________________GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG_GGAACUGGCCCCCGGUU
...(((((((.(((.(((.(((((.....))))).))).))).))).....................(((((((..(((((.....))))).)))))))(((.((......))))))))) (-35.12 = -35.40 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,760,588 – 6,760,686
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.34
Mean single sequence MFE -33.70
Consensus MFE -20.18
Energy contribution -20.74
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -2.06
Structure conservation index 0.60
SVM decision value 0.06
SVM RNA-class probability 0.563415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6760588 98 - 27905053
AACCGGGGGCCAGUUCC-CCCGACUAGGAGUCAAAUAAGUUGACAACCCAGUC---------------------GAGACCCCAAGACUCAGAAACUCUGAGACUUCAAGACCCGGCUGUC
...((((((......))-)))).......(((((.....)))))....(((((---------------------(.(.....(((.(((((.....))))).))).....).)))))).. ( -31.70)
>DroSec_CAF1 24831 98 - 1
AACCGGGGGCCAGUUCC-CCCGACUAGAAGUCAAAUAAGUUGACAACCCAGUC---------------------GAGACCCCAAGACUCAAAGACUCUGAGACUUCAAGACCCGGCUGUC
...((((((......))-)))).......(((((.....)))))....(((((---------------------(.(.....(((.((((.......)))).))).....).)))))).. ( -27.70)
>DroSim_CAF1 29205 98 - 1
AACCGGGGGCCAGUUCC-CCCGACUAGAAGUCAAAUAAGUUGACAACCCAGUC---------------------GAGACCCCAAGACUCAGAGACUCUGAGACUUCAAGACCCGGCUGUC
...((((((......))-)))).......(((((.....)))))....(((((---------------------(.(.....(((.(((((.....))))).))).....).)))))).. ( -31.70)
>DroEre_CAF1 9291 106 - 1
AACCGGGGGCCAGUUCCCCCCGACUGGAACUCAAAUAAGUUGACAACCCAGCCGGGC--------------CCCGAGACCCCAGGACUCAGAGACUCUGAGACUUCAAGACCCGGCUGUC
...((((((.......))))))...((...((((.....))))...))((((((((.--------------.((.........)).(((((.....))))).........)))))))).. ( -37.70)
>DroYak_CAF1 21385 120 - 1
AACCGGGGGCCACUUUCCCCUCGCCAGGAGUCAAAUAAGUUGACAACCCAGCCGAGUCCCGAGUACCGAGUCCCGAGACCCCAGGACUAAGAUACUCUGAGACUUCAAGACCCGGCUGUC
....(((((......)))))..(((.((.(((......((((......)))).((((((.((((((..(((((.(......).)))))..).))))).).)))))...)))))))).... ( -39.70)
>consensus
AACCGGGGGCCAGUUCC_CCCGACUAGAAGUCAAAUAAGUUGACAACCCAGUC_____________________GAGACCCCAAGACUCAGAGACUCUGAGACUUCAAGACCCGGCUGUC
..((((((((.((((......))))....(((((.....)))))......))).............................(((.(((((.....))))).))).....)))))..... (-20.18 = -20.74 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,760,628 – 6,760,726
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.53
Mean single sequence MFE -46.40
Consensus MFE -35.94
Energy contribution -35.98
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -1.97
Structure conservation index 0.77
SVM decision value 0.83
SVM RNA-class probability 0.860398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6760628 98 + 27905053
GGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUCCUAGUCGGG-GGAACUGGCCCCCGGUUAUGGCAUCCACUGGUUGCCCGGGGGUCCGCAGUUGAGCUC
..((((---------------------(((((((..(((((.....))))).))))))))))-).(((((((((((((.....(((.((...)).)))))))))))...)))))...... ( -45.80)
>DroSec_CAF1 24871 98 + 1
GGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG-GGAACUGGCCCCCGGUUAUGGCCUCCACUGGUUGCCCGGGGGUCCGCAGUUGAGCUC
..((((---------------------(((((((..(((((.....))))).))))))))))-).(((((((((((((...(((((......))))).))))))))...)))))...... ( -44.30)
>DroSim_CAF1 29245 98 + 1
GGUCUC---------------------GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG-GGAACUGGCCCCCGGUUAUGGCCUCCACUGGUUGCCCGGGGGUCCGCAGUUGAGCUC
..((((---------------------(((((((..(((((.....))))).))))))))))-).(((((((((((((...(((((......))))).))))))))...)))))...... ( -44.30)
>DroEre_CAF1 9331 106 + 1
GGUCUCGGG--------------GCCCGGCUGGGUUGUCAACUUAUUUGAGUUCCAGUCGGGGGGAACUGGCCCCCGGUUAUGGCCUCCACUGGUUGCCCGAGGGUCCGCAGUUGAGCUC
((.((((((--------------(((((((((((...((((.....))))..))))))))(((((......)))))......)))).))((((...(((....)))...)))).))))). ( -45.40)
>DroYak_CAF1 21425 120 + 1
GGUCUCGGGACUCGGUACUCGGGACUCGGCUGGGUUGUCAACUUAUUUGACUCCUGGCGAGGGGAAAGUGGCCCCCGGUUAUGGCCUCCACUGGUUGCCCGGGGGUCCGCAGUUGAGCUC
(((((((((........)))))))))..((..((..(((((.....))))).))..))(((..((..(((((((((((...(((((......))))).))))))).))))..))...))) ( -52.20)
>consensus
GGUCUC_____________________GACUGGGUUGUCAACUUAUUUGACUUCUAGUCGGG_GGAACUGGCCCCCGGUUAUGGCCUCCACUGGUUGCCCGGGGGUCCGCAGUUGAGCUC
((.(((.....................(((((((..(((((.....))))).)))))))......(((((((((((((...(((((......))))).))))))))...)))))))))). (-35.94 = -35.98 +   0.04)

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 10:35:16 2006