Locus 2281

Sequence ID 2L_DroMel_CAF1
Location 6,173,348 – 6,173,506
Length 158
Max. P 0.999627
window3662 window3663 window3664

overview

Window 2

Location 6,173,348 – 6,173,467
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.99
Mean single sequence MFE -33.77
Consensus MFE -31.72
Energy contribution -31.92
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.94
SVM decision value 1.11
SVM RNA-class probability 0.916989
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6173348 119 + 22407834
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUU-UGUGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCGUAGCCAC
.........((((.(.(((.(((.........)))-.))).).))))(((((((.....))))(((.((((((....)))))).)))...((((..............))))...))).. ( -28.64)
>DroSec_CAF1 9676 119 + 1
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUU-UGGGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCGUAGCCAC
.........((((.((........))))))...((-((((((((((((((.((((......)))))))(((((....))))))))))...)))))))).........((((....)))). ( -34.80)
>DroSim_CAF1 19052 119 + 1
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUU-UGGGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCGUAGCCAC
.........((((.((........))))))...((-((((((((((((((.((((......)))))))(((((....))))))))))...)))))))).........((((....)))). ( -34.80)
>DroEre_CAF1 9144 119 + 1
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUU-UGGGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCGUAGCCAC
.........((((.((........))))))...((-((((((((((((((.((((......)))))))(((((....))))))))))...)))))))).........((((....)))). ( -34.80)
>DroYak_CAF1 19367 120 + 1
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUUUUGGGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCAUAGCCAC
.........((((.((........))))))...(((((((((((((((((.((((......)))))))(((((....))))))))))...)))))))))........((((....)))). ( -35.80)
>consensus
AAUUUAUUCGACACGCCACUGAGAGCUGUUCACUU_UGGGCCAUGUCGGUGAUGAAAAACGUCAUGCCAGCAAAUUGUUGCUGACAUAAAGGCCCAAGACCAAAACAUGGCCGUAGCCAC
.........((((.((........))))))......((((((((((((((.((((......)))))))(((((....))))))))))...))))))...........((((....)))). (-31.72 = -31.92 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,173,348 – 6,173,467
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.99
Mean single sequence MFE -42.22
Consensus MFE -40.58
Energy contribution -40.62
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.83
Structure conservation index 0.96
SVM decision value 3.80
SVM RNA-class probability 0.999627
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6173348 119 - 22407834
GUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCACA-AAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
..((((..(((((.....)))))...)))).((((((((((((....)))))))))))).............(((((((.(((.-.((.(.....).))..))).)))))))........ ( -44.10)
>DroSec_CAF1 9676 119 - 1
GUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCCCA-AAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
...((((((((((((((..(((..((((.(.((((((((((((....)))))))))))).)...))))..))))))))))))..-..(....)........))))).............. ( -42.10)
>DroSim_CAF1 19052 119 - 1
GUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCCCA-AAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
...((((((((((((((..(((..((((.(.((((((((((((....)))))))))))).)...))))..))))))))))))..-..(....)........))))).............. ( -42.10)
>DroEre_CAF1 9144 119 - 1
GUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCCCA-AAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
...((((((((((((((..(((..((((.(.((((((((((((....)))))))))))).)...))))..))))))))))))..-..(....)........))))).............. ( -42.10)
>DroYak_CAF1 19367 120 - 1
GUGGCUAUGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCCCAAAAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
..((((..(((((.....)))))...)))).((((((((((((....)))))))))))).............(((((((.(((...(((.....)))....).)))))))))........ ( -40.70)
>consensus
GUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGGCCCA_AAGUGAACAGCUCUCAGUGGCGUGUCGAAUAAAUU
...((((((((((((((..(((..((((.(.((((((((((((....)))))))))))).)...))))..)))))))))))).....(....)........))))).............. (-40.58 = -40.62 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,173,387 – 6,173,506
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.04
Mean single sequence MFE -45.26
Consensus MFE -39.32
Energy contribution -39.60
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -2.68
Structure conservation index 0.87
SVM decision value 3.53
SVM RNA-class probability 0.999353
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6173387 119 - 22407834
GCGGGGUGUGG-GGGCGGGUAAACAAAGUACGAAGUGGGCGUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
.(((((((.((-((((((((...(((.(.((.(((...(((((((....)))))))))).)))))).))).((((((((((((....))))))))))))))))))))))).)))...... ( -47.20)
>DroSec_CAF1 9715 118 - 1
--GGAGUGUGUGGGGCGGGUAAACAAAGUAGGAAGUGGGCGUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
--.....((((.((...((.((((....(((((...(((((((((....)))))))))...))))).....((((((((((((....)))))))))))).)))).))....)).)))).. ( -44.80)
>DroSim_CAF1 19091 117 - 1
--GGAGUGUAA-GGGCGGGUAAACAAAGUACGAAGUGGGCGUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
--((.(((.((-((((((((...(((.(.((.(((...(((((((....)))))))))).)))))).))).((((((((((((....))))))))))))))))))))))..))....... ( -42.70)
>DroEre_CAF1 9183 119 - 1
GGGGAGUGUGG-AGGCGGGUAUACAAAGUACAAAGUGGGCGUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
.((..(((.((-((((((((...(((.(.((.....(((((((((....)))))))))..)))))).))).((((((((((((....))))))))))))))))))))))..))....... ( -45.50)
>DroYak_CAF1 19407 118 - 1
GUGGGGUG-GU-AGGCGGGCAUACAAAGUACAAAGUGGGCGUGGCUAUGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
((((((((-(.-((((((((...(((.(.((.....(((((((((....)))))))))..)))))).))).((((((((((((....))))))))))))))))).))))).)).)).... ( -46.10)
>consensus
G_GGAGUGUGG_GGGCGGGUAAACAAAGUACGAAGUGGGCGUGGCUACGGCCAUGUUUUGGUCUUGGGCCUUUAUGUCAGCAACAAUUUGCUGGCAUGACGUUUUUCAUCACCGACAUGG
..((...((((.((((((((...(((....((((....(((((((....)))))))))))...))).))).((((((((((((....))))))))))))))))).))))..))....... (-39.32 = -39.60 +   0.28)

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 10:23:58 2006