Locus 3214

Sequence ID 2R_DroMel_CAF1
Location 10,975,229 – 10,975,457
Length 228
Max. P 0.854696
window5285 window5286 window5287

overview

Window 5

Location 10,975,229 – 10,975,325
Length 96
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 76.98
Mean single sequence MFE -25.64
Consensus MFE -13.70
Energy contribution -14.98
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.53
SVM decision value 0.80
SVM RNA-class probability 0.854696
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10975229 96 + 20766785
GCGCACAUAAUUAGCGCCACAGCUCUUGGCGCUGCACACUGGCAACUAGCAACUAGCAACCUGCAUCCGGCAACCUGCAACCAG-------CCAUCUGCAACA
..(((......((((((((.......)))))))).....((((.....((.....))....((((...(....).))))....)-------)))..))).... ( -26.60)
>DroSec_CAF1 87604 81 + 1
GCGCACAUAAUUAGCGCCACAGCUCUUGGCGCUGCACACUGGCAACUAGCA--------CCUGCAUC-GGCA--CUGCA-CCAG-------CAU--UGC-ACA
..((.......((((((((.......)))))))).......)).....((.--------...))...-.(((--.(((.-...)-------)).--)))-... ( -23.34)
>DroSim_CAF1 89887 96 + 1
GCGCACAUAAUUAGCGCCACAGCUCUUGGCGCUGCACACUGGCAACUAGCAACUAGCAACCUGCAUCCGGCAACCUGCAACCAG-------CCAUCUGCAACA
..(((......((((((((.......)))))))).....((((.....((.....))....((((...(....).))))....)-------)))..))).... ( -26.60)
>DroEre_CAF1 89951 95 + 1
GCGCACAUAAUUAGCGCCACAACUCUU--------ACACUGGCAACUGGGAGCCUGCAUCCUGCAACCUGCAACCUGCAACCAGCAAACUGCAAUCUGCAGCG
((((.........)))).....(((((--------(....(....)))))))........(((((...((((...(((.....)))...))))...))))).. ( -21.90)
>DroYak_CAF1 91510 96 + 1
GCGCACAUAAUUAGCGCCACAUCUCUUGGCGCUACACACUGGCAACUAGGAACCUGCAUCCUGCAACCUGCAAC-------CAGCAACCGGCAGUCUGCAACG
..((.......((((((((.......)))))))).......))...........((((..((((....(((...-------..)))....))))..))))... ( -29.74)
>consensus
GCGCACAUAAUUAGCGCCACAGCUCUUGGCGCUGCACACUGGCAACUAGCAACCAGCAACCUGCAUCCGGCAACCUGCAACCAG_______CAAUCUGCAACA
((((.......((((((((.......)))))))).......))..................(((.....))).........................)).... (-13.70 = -14.98 +   1.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,975,325 – 10,975,423
Length 98
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 76.22
Mean single sequence MFE -33.32
Consensus MFE -10.05
Energy contribution -11.30
Covariance contribution 1.25
Combinations/Pair 1.35
Mean z-score -2.64
Structure conservation index 0.30
SVM decision value 0.49
SVM RNA-class probability 0.758005
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10975325 98 + 20766785
UGGAAUGGGCAACUU--GCACCAA-GGCAGGCUGUAGCUGCAACAUUC-CCUGCGGUCUGUAGUUGCAUUAUUCCAAUUAGCAGUGUGCGAAUACAGCAGCG
((((((((((((((.--.......-.(((((((((((...........-.))))))))))))))))).))))))))....((.((((....)))).)).... ( -33.20)
>DroSec_CAF1 87685 83 + 1
UGA-AU--GCCACUU--GCAC--A-AGCA-GCUGUAGCUGCUAAAU---CCUGCGGUC-GUAGCUGCAU-AUUCC-AUUAGCAGUUCG--A--UCAGCAGCG
...-.(--((.....--))).--.-((((-((....))))))....---.((((((((-(.((((((.(-(....-..))))))))))--)--)).)))).. ( -29.90)
>DroSim_CAF1 89983 97 + 1
UGGAAUGGGCAAUUU--GCAGCAA-GGCA-GCUGUAGCUGCAACAUUC-CCUGCGGUCUGUAGCUGCAUUAUUCCAAUUAGCAGUGUGCGAAUACAUCAGCG
((((((((((.....--)).....-.(((-((((((((((((......-..))))).)))))))))).))))))))....((.(((((....)))))..)). ( -33.60)
>DroEre_CAF1 90046 97 + 1
UGGAAAGGGCAACUA--GCAGCAG-GGCA-AGUACAGCUGCAACAUUC-CCUGCGGUGUGUAGUCGCAUUAUUCCAAUUAGGAGUGUGUGAAUACAGCACCG
.((((.((....)).--(((((.(-....-....).)))))....)))-)...(((((((((.((((((.(((((.....))))))))))).)))).))))) ( -37.00)
>DroYak_CAF1 91606 97 + 1
UGGAAAGGGCAAUUG--ACAGCAA-GGCA-AGUACAGCUGCAACAUUC-CCUGCGGUCUGUAGUUGCAUUAUUCCAAUUAGGAGUGUGUGAAUGCAGCACCG
......((((.(((.--(((....-.(((-(.((((((((((......-..))))).))))).))))..((((((.....))))))))).)))...)).)). ( -33.00)
>DroAna_CAF1 90328 99 + 1
--GUAACUGCAACUGCAACUGCAAGUGCA-ACUGCAACGGCCACAUUCCCCUGCGGUCGUCAGCUGCAUUAUUCCAAUUAGGAAAGUGUAAAUGCAGCAAGG
--(((..((((..(((....)))..))))-..))).((((((.((......)).))))))..((((((((.((((.....))))......)))))))).... ( -33.20)
>consensus
UGGAAAGGGCAACUU__GCAGCAA_GGCA_ACUGCAGCUGCAACAUUC_CCUGCGGUCUGUAGCUGCAUUAUUCCAAUUAGCAGUGUGUGAAUACAGCAGCG
........((................(((.(((((((((((...........))))).)))))))))................((((....)))).)).... (-10.05 = -11.30 +   1.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,975,358 – 10,975,457
Length 99
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 78.09
Mean single sequence MFE -33.55
Consensus MFE -13.90
Energy contribution -14.60
Covariance contribution 0.70
Combinations/Pair 1.29
Mean z-score -2.39
Structure conservation index 0.41
SVM decision value 0.34
SVM RNA-class probability 0.695832
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10975358 99 + 20766785
GCUGCAACAUUC-CCUGCGGUCUGUAGUUGCAUUAUUCCAAUUAGCAGUGUGCGAAUACAGCAGCGUACUGAUUGAUUGCAGAAUGCCUGUUGCGGUUGU------
(((((((((...-.((((.....))))..(((((....(((((((((((((((..........)))))))).)))))))...))))).)))))))))...------ ( -32.20)
>DroSec_CAF1 87712 87 + 1
GCUGCUAAAU---CCUGCGGUC-GUAGCUGCAU-AUUCC-AUUAGCAGUUCG--A--UCAGCAGCGUA-UGA-UGAUUGCAGAACGUCUGUUGCAGUGU-------
(((((...((---.((((((((-(.((((((.(-(....-..))))))))))--)--)).)))).)).-...-.....((((.....)))).)))))..------- ( -29.20)
>DroSim_CAF1 90015 99 + 1
GCUGCAACAUUC-CCUGCGGUCUGUAGCUGCAUUAUUCCAAUUAGCAGUGUGCGAAUACAUCAGCGUACUGAUUGAUUGCAGAAUGCCUGUGGCGGUUGC------
((..((.(((((-..((((((.....))))))......(((((((((((((((..........)))))))).)))))))..)))))..))..))......------ ( -31.30)
>DroEre_CAF1 90078 99 + 1
GCUGCAACAUUC-CCUGCGGUGUGUAGUCGCAUUAUUCCAAUUAGGAGUGUGUGAAUACAGCACCGAACUGAUUGAUUGCAGGAUGUCUGUUGCGGUUGU------
(((((((((..(-(((((((((((((.((((((.(((((.....))))))))))).)))).))))...(.....)...)))))..)..)))))))))...------ ( -41.20)
>DroYak_CAF1 91638 99 + 1
GCUGCAACAUUC-CCUGCGGUCUGUAGUUGCAUUAUUCCAAUUAGGAGUGUGUGAAUGCAGCACCGAACUGAUUGAUUGCAGAAUGUGAGUUGCGGUUGU------
((((((((....-....(((((((((.(..(((.(((((.....))))))))..).))))).))))..(((........))).......))))))))...------ ( -35.00)
>DroAna_CAF1 90361 106 + 1
ACGGCCACAUUCCCCUGCGGUCGUCAGCUGCAUUAUUCCAAUUAGGAAAGUGUAAAUGCAGCAAGGCACUGAUUGAUUGGAGAUUGCCUUCAGGACUGCCUCAUCC
((((((.((......)).))))))..((((((((.((((.....))))......)))))))).(((((....((((..((......)).))))...)))))..... ( -32.40)
>consensus
GCUGCAACAUUC_CCUGCGGUCUGUAGCUGCAUUAUUCCAAUUAGCAGUGUGUGAAUACAGCAGCGUACUGAUUGAUUGCAGAAUGCCUGUUGCGGUUGU______
(((((..........(((((.......)))))......(((((((.....(((.......))).....)))))))...((((.....)))).)))))......... (-13.90 = -14.60 +   0.70)

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 10:50:14 2006