Locus 5216

Sequence ID 2L_DroMel_CAF1
Location 14,744,410 – 14,744,614
Length 204
Max. P 0.795811
window8304 window8305 window8306

overview

Window 4

Location 14,744,410 – 14,744,523
Length 113
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.14
Mean single sequence MFE -35.25
Consensus MFE -22.16
Energy contribution -23.05
Covariance contribution 0.89
Combinations/Pair 1.19
Mean z-score -2.06
Structure conservation index 0.63
SVM decision value 0.51
SVM RNA-class probability 0.762758
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14744410 113 - 22407834
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUUGCUUUCUGCUUGCCAGAGACAGAAAGGGCUAACCAACACUGUUACACUACAGUGCUGGGAGUGG------
((((((.......))))))...(((.(((((((....(((...(((((((.((((((.....)))))))))))))))).))))..((((((......))))))...)))))).------ ( -39.60)
>DroPse_CAF1 22842 94 - 1
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUU------UGCAUGACAGACACAGAGGCAA--AGGCAAUA----------GCAG---UGGCAGUGG----CA
((((((.......))))))..((((..((.((((((((((((.(.....------.).))))))).....)))))..--.)).....----------((..---..)).))))----.. ( -26.40)
>DroSec_CAF1 8588 113 - 1
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUUGCAUUCUGCUUGCCAGAGAUAGAAAGGGCUAACCAACACUGUUACACUGCAGUGCUGGGAGUGG------
((((((.......))))))...(((.(((((((((((.((..(((((..(((.......))).)))))..)).))))..))))..((((((......))))))...)))))).------ ( -37.80)
>DroSim_CAF1 8225 113 - 1
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUUGCUUUCUGCUUGCCAGAGACAGAAAGGGCUAACCAACACUGUUACACUGCAGUGCUGGGAGUGG------
((((((.......))))))...(((.(((((((....(((...(((((((.((((((.....)))))))))))))))).))))..((((((......))))))...)))))).------ ( -39.90)
>DroEre_CAF1 8339 119 - 1
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUUGCUUUCUGCUUGCCAGAGACAGAAAGGGCUAACCAACACUGUUGCAGUGCAGUGCUGGCAGUGGAGGGGA
((((((.......))))))..............((((.((..((((((((.((((((.....))))))))))))))(((..(((.((((((......)))))).))).))).)).)))) ( -41.40)
>DroPer_CAF1 22692 94 - 1
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUU------UGCAUGACAGACACAGAGGCAA--AGGCAAUA----------GCAG---UGGCAGUGG----CA
((((((.......))))))..((((..((.((((((((((((.(.....------.).))))))).....)))))..--.)).....----------((..---..)).))))----.. ( -26.40)
>consensus
GCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUCAUUCUUUUUGCUUUCUGCUUGCCAGAGACAGAAAGGGCUAACCAACACUGUUACACUGCAGUGCUGGCAGUGG______
((((((.......))))))...(((..(((((...((((..(((((((((...((((.....))))..)))))))))....................)))).)))))..)))....... (-22.16 = -23.05 +   0.89)

alignment

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secondary structure

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Window 5

Location 14,744,483 – 14,744,601
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.11
Mean single sequence MFE -32.77
Consensus MFE -28.13
Energy contribution -28.68
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.86
SVM decision value 0.60
SVM RNA-class probability 0.795811
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14744483 118 - 22407834
ACUGCAACCAGCAGU--GUGGCAGUGCCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((.....)))))--..(((((.(((...........(((....((((((.....))))))...)))..........(((((((.......))))))).........)))...))))) ( -34.20)
>DroPse_CAF1 22896 120 - 1
GCUGCAAGCGGCAGCCAGAGGCAGCAACAGCAACAAGAACAGCAAAGCACACAUCCGGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((..((....)).....))))).((((.(((..((.(((....((((((.....))))))...)))..........(((((((.......)))))))......))..)))..)))). ( -34.20)
>DroEre_CAF1 8418 118 - 1
ACUGCAACCAGCAGU--GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((.....)))))--..(((((.((.(((...(((..(((....((((((.....))))))...)))..........(((((((.......)))))))....)))...)))))))))) ( -33.90)
>DroYak_CAF1 9962 115 - 1
---GCAACCAGCAGU--GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
---..((((.(..((--((((((.((....))...))..(((....((((((.....))))))...)))..........(((((((.......))))))).))))))).))))....... ( -29.50)
>DroAna_CAF1 29233 113 - 1
ACUGCAACCAGCA-------GCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((........-------)))))((.(((...(((..(((....((((((.....))))))...)))..........(((((((.......)))))))....)))...))).)).... ( -30.60)
>DroPer_CAF1 22746 120 - 1
GCUGCAAGCGGCAGCCAGAGGCAGCAACAGCAACAAGAACAGCAAAGCACACAUCCGGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((..((....)).....))))).((((.(((..((.(((....((((((.....))))))...)))..........(((((((.......)))))))......))..)))..)))). ( -34.20)
>consensus
ACUGCAACCAGCAGU__GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUUGCAUGCACAAAAGGCAUGCACUCACAUCCGGUUUCCUGUC
(((((.....)))))....(((((.(((...........(((....((((((.....))))))...)))..........(((((((.......)))))))..........)))..))))) (-28.13 = -28.68 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,744,523 – 14,744,614
Length 91
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.36
Mean single sequence MFE -24.73
Consensus MFE -14.05
Energy contribution -14.22
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.57
SVM decision value 0.37
SVM RNA-class probability 0.710474
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14744523 91 - 22407834
--------------CCAGAAGCCA-------GCAACUGCAACCAGCAGU--GUGGCAGUGCCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUU
--------------...(((((((-------...(((((.....)))))--.)))).................(((....((((((.....))))))...))).....)))... ( -24.30)
>DroPse_CAF1 22936 92 - 1
---------------CACAAGCGG-------ACUGCUGCAAGCGGCAGCCAGAGGCAGCAACAGCAACAAGAACAGCAAAGCACACAUCCGGUGUGUCAACUGAAUAAUUCGUU
---------------....(((((-------.((((((....)))))))).(((...((....))........(((....((((((.....))))))...))).....)))))) ( -24.50)
>DroEre_CAF1 8458 98 - 1
--------------CCAGCAGCCAACAGCCAGCAACUGCAACCAGCAGU--GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUU
--------------..(((.((((...((((...(((((.....)))))--.))))..))))...........(((....((((((.....))))))...)))........))) ( -30.30)
>DroYak_CAF1 10002 85 - 1
--------------CCAGCAGCCA-------------GCAACCAGCAGU--GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUU
--------------..(((.((((-------------.(..(((.....--.)))..)))))...........(((....((((((.....))))))...)))........))) ( -18.20)
>DroAna_CAF1 29273 107 - 1
GCGGCAACUGGCAACCAGCAACCGGCAACCAGCAACUGCAACCAGCA-------GCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUU
.(((...((((...))))...))).......((.(((((........-------))))).))...........(((....((((((.....))))))...)))........... ( -26.60)
>DroPer_CAF1 22786 92 - 1
---------------CACAAGCGG-------ACUGCUGCAAGCGGCAGCCAGAGGCAGCAACAGCAACAAGAACAGCAAAGCACACAUCCGGUGUGUCAACUGAAUAAUUCGUU
---------------....(((((-------.((((((....)))))))).(((...((....))........(((....((((((.....))))))...))).....)))))) ( -24.50)
>consensus
______________CCAGAAGCCA_______GCAACUGCAACCAGCAGU__GUGGCAGUGGCAACAACAUGAACAGCAAAGCACACAUCCUGUGUGUCAACUGAAUAAUUCGUU
..................................(((((.....)))))........((....))........(((....((((((.....))))))...)))........... (-14.05 = -14.22 +   0.17)

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 11:38:54 2006