Locus 1944

Sequence ID 2L_DroMel_CAF1
Location 5,256,800 – 5,256,958
Length 158
Max. P 0.901470
window3144 window3145 window3146

overview

Window 4

Location 5,256,800 – 5,256,892
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 81.86
Mean single sequence MFE -23.83
Consensus MFE -13.87
Energy contribution -13.23
Covariance contribution -0.64
Combinations/Pair 1.22
Mean z-score -2.43
Structure conservation index 0.58
SVM decision value 0.41
SVM RNA-class probability 0.724537
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5256800 92 - 22407834
UAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUCG------CCGACUCCAACUGAAAUGGGAAAUGGAAGUGCAAAUGGAAAUGGCAAUGGCAAU
..(((((((((((....)))))))))))....((((.(------(((..(((((((...((.....))...))).....))))..))))...)))).. ( -24.10)
>DroPse_CAF1 32524 92 - 1
UAGUGCAAAGUCGUGUCUGAUUUUGCAUAAAAUGUCGGGGAUUCUCGACUAAAAUUGAAAUUGGAAAUGGCAGUGCAAAUGGAAAUGG------AAAU
...((((..(((((.((..(((((.........((((((....)))))).......)))))..)).)))))..))))...........------.... ( -24.69)
>DroSec_CAF1 33608 92 - 1
UAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUCG------CCGUCUCCAACUGAAAUGGGAAAUGGAAGUGCAAAUGGAAAUGGCAACGGCAAU
..(((((((((((....)))))))))))....((((.(------((((.(((((((...((.....))...))).....)))).)))))))))..... ( -27.50)
>DroEre_CAF1 26724 92 - 1
UAGUGCAAAGUCGUGUUCGAUUUUGCAUAAAAUGUUCG------CCGACUCCAGCUGAAAUGGGAAAUGGAAGUGCAAAUGGCAAUGGAAAUGGAAAU
..(((((((((((....))))))))))).........(------(((((((((.((......))...))).))).....))))............... ( -23.20)
>DroYak_CAF1 35658 80 - 1
UAGUGCAAAGUCGUGUUCGAUUUUGCAUAAAAUGUUCG------CCGACUUCAACUGAAAUGGGAAAUGGAAGUGCAAA------------UGGAAAU
..(((((((((((....))))))))))).........(------(..(((((..((.....))......)))))))...------------....... ( -18.80)
>DroPer_CAF1 32611 92 - 1
UAGUGCAAAGUCGUGUCUGAUUUUGCAUAAAAUGUCGGGGAUUCUCGACUAAAAUUGAAAUUGGAAAUGGCAGUGCAAAUGAAAAUGG------AAAU
...((((..(((((.((..(((((.........((((((....)))))).......)))))..)).)))))..))))...........------.... ( -24.69)
>consensus
UAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUCG______CCGACUCCAACUGAAAUGGGAAAUGGAAGUGCAAAUGGAAAUGG___UGGAAAU
..(((((((((((....)))))))))))................(((..((((.......))))...)))............................ (-13.87 = -13.23 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,256,855 – 5,256,958
Length 103
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.08
Mean single sequence MFE -25.32
Consensus MFE -13.68
Energy contribution -14.27
Covariance contribution 0.59
Combinations/Pair 1.09
Mean z-score -1.78
Structure conservation index 0.54
SVM decision value -0.01
SVM RNA-class probability 0.526374
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5256855 103 + 22407834
GAACAUUUUAUGCAAAAUCGGACACGACUUUGCACUAAAAA---UUAAGCGAU-CCCGCAGAGAAACUUUGACCAGGGUGUCCAAAAAGGAAAGA--------UACAUCACUACU
.....(((((((((((.(((....))).)))))).))))).---...((.(((-(((.(((((...)))))....)))..(((.....)))....--------...))).))... ( -21.70)
>DroSec_CAF1 33663 111 + 1
GAACAUUUUAUGCAAAAUCGGACACGACUUUGCACUAAAAA---UGAAGCGAU-CCCGCAGAGAAACUUUGACUAGGCUGGCCAAAAAGGGAGGAGCACUAUAAACAGCACUACU
...((((((.((((((.(((....))).))))))...))))---))..((..(-(((.(((((...)))))....((....)).....))))...)).................. ( -27.20)
>DroSim_CAF1 35160 111 + 1
GAACAUUUUAUGCAAAAUCGGACACGACUUUGCACUAAAAA---UGAAGCGAU-CCCGCAGAGAAACUUUGACCAGGCUGGCCAAAAAGGGAGGAGCACUAUAAACAUCACUACU
((.((((((.((((((.(((....))).))))))...))))---))..((..(-(((.(((((...)))))....((....)).....))))...))..........))...... ( -27.30)
>DroEre_CAF1 26779 103 + 1
GAACAUUUUAUGCAAAAUCGAACACGACUUUGCACUAAAAA---UUAAGCGAU-CCCGCAGAGAAACUUUGACCAGGAUGGCCAAAAAGACAGC--------AUAGAGCACUACU
.....(((((((((((.(((....))).)))))).))))).---....((.((-((..(((((...)))))....)))).))..........((--------.....))...... ( -21.80)
>DroYak_CAF1 35701 108 + 1
GAACAUUUUAUGCAAAAUCGAACACGACUUUGCACUAAAAA---UGAAGCGAU-CCCGCAGAGAAACUUUGACCAGGGUGGCCAAAAGGGUAGGC-CACU--AGGCUGCACUACU
...((((((.((((((.(((....))).))))))...))))---))..(((..-(((.(((((...)))))....))((((((.........)))-))).--.)..)))...... ( -30.10)
>DroPer_CAF1 32666 97 + 1
CGACAUUUUAUGCAAAAUCAGACACGACUUUGCACUAAAAAAACCUAAACGAGACCCUGAGAGGAGC--GGCCCAGGGUGGCCCAAAGCC--UGA--------AGUCUG------
.(((.(((((((((((.((......)).)))))).))))).............((((((...((...--..))))))))(((.....)))--...--------.)))..------ ( -23.80)
>consensus
GAACAUUUUAUGCAAAAUCGGACACGACUUUGCACUAAAAA___UGAAGCGAU_CCCGCAGAGAAACUUUGACCAGGGUGGCCAAAAAGGGAGGA_______AAACAGCACUACU
.....(((((((((((.(((....))).)))))).)))))........(((.....)))........((((.((.....)).))))............................. (-13.68 = -14.27 +   0.59)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,256,855 – 5,256,958
Length 103
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.08
Mean single sequence MFE -30.47
Consensus MFE -19.55
Energy contribution -20.30
Covariance contribution 0.75
Combinations/Pair 1.09
Mean z-score -2.04
Structure conservation index 0.64
SVM decision value 1.02
SVM RNA-class probability 0.901470
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5256855 103 - 22407834
AGUAGUGAUGUA--------UCUUUCCUUUUUGGACACCCUGGUCAAAGUUUCUCUGCGGG-AUCGCUUAA---UUUUUAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUC
...((((((...--------....(((.....)))..((((((...........))).)))-))))))...---......(((((((((((....)))))))))))......... ( -24.30)
>DroSec_CAF1 33663 111 - 1
AGUAGUGCUGUUUAUAGUGCUCCUCCCUUUUUGGCCAGCCUAGUCAAAGUUUCUCUGCGGG-AUCGCUUCA---UUUUUAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUC
.(.((..(((....)))..)).)((((..((((((.......))))))((......)))))-)......((---((((..(((((((((((....)))))))))))))))))... ( -30.30)
>DroSim_CAF1 35160 111 - 1
AGUAGUGAUGUUUAUAGUGCUCCUCCCUUUUUGGCCAGCCUGGUCAAAGUUUCUCUGCGGG-AUCGCUUCA---UUUUUAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUC
...(((((.((.......))...((((..(((((((.....)))))))((......)))))-)))))).((---((((..(((((((((((....)))))))))))))))))... ( -32.20)
>DroEre_CAF1 26779 103 - 1
AGUAGUGCUCUAU--------GCUGUCUUUUUGGCCAUCCUGGUCAAAGUUUCUCUGCGGG-AUCGCUUAA---UUUUUAGUGCAAAGUCGUGUUCGAUUUUGCAUAAAAUGUUC
...((((.(((.(--------((.(...((((((((.....))))))))...)...)))))-).))))...---......(((((((((((....)))))))))))......... ( -30.10)
>DroYak_CAF1 35701 108 - 1
AGUAGUGCAGCCU--AGUG-GCCUACCCUUUUGGCCACCCUGGUCAAAGUUUCUCUGCGGG-AUCGCUUCA---UUUUUAGUGCAAAGUCGUGUUCGAUUUUGCAUAAAAUGUUC
......((.(((.--...)-))...(((.(((((((.....)))))))((......)))))-...))..((---((((..(((((((((((....)))))))))))))))))... ( -35.20)
>DroPer_CAF1 32666 97 - 1
------CAGACU--------UCA--GGCUUUGGGCCACCCUGGGCC--GCUCCUCUCAGGGUCUCGUUUAGGUUUUUUUAGUGCAAAGUCGUGUCUGAUUUUGCAUAAAAUGUCG
------..(((.--------...--(((.....)))((((((((..--......))))))))..................(((((((((((....))))))))))).....))). ( -30.70)
>consensus
AGUAGUGAUGUUU_______UCCUCCCUUUUUGGCCACCCUGGUCAAAGUUUCUCUGCGGG_AUCGCUUAA___UUUUUAGUGCAAAGUCGUGUCCGAUUUUGCAUAAAAUGUUC
............................((((((((.....)))))))).......(((.....))).............(((((((((((....)))))))))))......... (-19.55 = -20.30 +   0.75)

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 10:15:36 2006