Locus 4278

Sequence ID 2L_DroMel_CAF1
Location 12,227,855 – 12,227,945
Length 90
Max. P 0.820465
window6747 window6748

overview

Window 7

Location 12,227,855 – 12,227,945
Length 90
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 79.65
Mean single sequence MFE -30.33
Consensus MFE -15.70
Energy contribution -16.07
Covariance contribution 0.36
Combinations/Pair 1.24
Mean z-score -2.39
Structure conservation index 0.52
SVM decision value 0.68
SVM RNA-class probability 0.820465
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12227855 90 + 22407834
------CGCCAGCCAAUGGAAAAGCACAUCGUGUGCUAUGGAAACGGUUUGACCAGCUGGCACAAAUGAAUG--GC-------------GGCAGAGGGAAAAUUGGACUGA
------...((((((((((...(((((.....))))).((....))......)).((((.((........))--.)-------------))).........))))).))). ( -26.30)
>DroSec_CAF1 51387 90 + 1
------UGCCAGCCAAUGGAAAAGCACAUCGUGUGCUAUGGAAACGGUUUGACCAGCUGGCACAAAUGAAUGGGGC-------------GGCU--GGGAAAAUUGGACCGA
------..(((.....)))...(((((.....))))).(((...((((((..(((((((.(.((......)).).)-------------))))--))..))))))..))). ( -31.90)
>DroSim_CAF1 52171 88 + 1
------UGCCAGCCAAUGGAAAAGCACAUCGUGUGCUAUGGAAAUGGUUUGACCAGCUGGCACAAAUGAAUG--GC-------------GGCU--GGGAAAAUUGGACCGA
------..(((.....)))...(((((.....))))).(((...((((((..(((((((.((........))--.)-------------))))--))..))))))..))). ( -29.50)
>DroEre_CAF1 49339 88 + 1
------UGCCAGCCAAUGGAAAAGCACAUUGUGUGCCAUGGAAACGGUUUGACCAGCUGGCACAAAUGAAUG--GC-------------GGCA--GGGAAAAUUGGCCCGA
------((((.((((.((......))((((.(((((((.(....)((.....))...)))))))))))..))--))-------------))))--(((........))).. ( -31.80)
>DroYak_CAF1 50302 88 + 1
------CACCAGCCAAUGGAAAAGCACGUUGUGUGCUAUGCAAACGAUUUGACCAGCUGGCACAAAUGAAUG--GC-------------GGCA--GGGAAAAUCGGACCGA
------..(((.....)))...(((((.....))))).......((((((..((.((((.((........))--.)-------------))).--))..))))))...... ( -26.50)
>DroAna_CAF1 47259 107 + 1
UUGUGAUGUCCGCAAACGGAGAAUAAUUUUGUGUACUGUGGCAACUGUUUGGCCAGCUGGCACAAAUGUUUG--GCCAAAAGGCGGGCAGGCG--GGCAAAAAAGGCCUGG
......(((((((....((.(((((..(((((((....((((.........))))....)))))))))))).--.)).....)))))))..((--(((.......))))). ( -36.00)
>consensus
______UGCCAGCCAAUGGAAAAGCACAUCGUGUGCUAUGGAAACGGUUUGACCAGCUGGCACAAAUGAAUG__GC_____________GGCA__GGGAAAAUUGGACCGA
.......((((((...(((...(((((.....)))))..(....).......)))))))))..................................((..........)).. (-15.70 = -16.07 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,227,855 – 12,227,945
Length 90
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 79.65
Mean single sequence MFE -24.34
Consensus MFE -15.25
Energy contribution -15.31
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -1.75
Structure conservation index 0.63
SVM decision value 0.47
SVM RNA-class probability 0.747128
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12227855 90 - 22407834
UCAGUCCAAUUUUCCCUCUGCC-------------GC--CAUUCAUUUGUGCCAGCUGGUCAAACCGUUUCCAUAGCACACGAUGUGCUUUUCCAUUGGCUGGCG------
...................(((-------------((--((....((((.(((....)))))))..........(((((.....))))).......)))).))).------ ( -21.20)
>DroSec_CAF1 51387 90 - 1
UCGGUCCAAUUUUCCC--AGCC-------------GCCCCAUUCAUUUGUGCCAGCUGGUCAAACCGUUUCCAUAGCACACGAUGUGCUUUUCCAUUGGCUGGCA------
.((((...........--.)))-------------).............((((((((((.....))........(((((.....)))))........))))))))------ ( -23.30)
>DroSim_CAF1 52171 88 - 1
UCGGUCCAAUUUUCCC--AGCC-------------GC--CAUUCAUUUGUGCCAGCUGGUCAAACCAUUUCCAUAGCACACGAUGUGCUUUUCCAUUGGCUGGCA------
((((.(((((....((--(((.-------------((--((......)).))..)))))...............(((((.....))))).....)))))))))..------ ( -23.40)
>DroEre_CAF1 49339 88 - 1
UCGGGCCAAUUUUCCC--UGCC-------------GC--CAUUCAUUUGUGCCAGCUGGUCAAACCGUUUCCAUGGCACACAAUGUGCUUUUCCAUUGGCUGGCA------
..(((........)))--.(((-------------((--((..(((((((((((..(((...........)))))))))).))))...........)))).))).------ ( -26.62)
>DroYak_CAF1 50302 88 - 1
UCGGUCCGAUUUUCCC--UGCC-------------GC--CAUUCAUUUGUGCCAGCUGGUCAAAUCGUUUGCAUAGCACACAACGUGCUUUUCCAUUGGCUGGUG------
((((((((((((..((--.((.-------------((--((......)).))..)).))..)))))).......(((((.....)))))........))))))..------ ( -23.30)
>DroAna_CAF1 47259 107 - 1
CCAGGCCUUUUUUGCC--CGCCUGCCCGCCUUUUGGC--CAAACAUUUGUGCCAGCUGGCCAAACAGUUGCCACAGUACACAAAAUUAUUCUCCGUUUGCGGACAUCACAA
.(((((..........--.)))))...(((....)))--.......(((((.((((((......)))))).)))))...............((((....))))........ ( -28.20)
>consensus
UCGGUCCAAUUUUCCC__UGCC_____________GC__CAUUCAUUUGUGCCAGCUGGUCAAACCGUUUCCAUAGCACACAAUGUGCUUUUCCAUUGGCUGGCA______
.................................................(((((((..((..............(((((.....))))).....))..)))))))...... (-15.25 = -15.31 +   0.06)

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 11:14:02 2006