Locus 2909

Sequence ID 3L_DroMel_CAF1
Location 8,293,004 – 8,293,187
Length 183
Max. P 0.776574
window4541 window4542 window4543

overview

Window 1

Location 8,293,004 – 8,293,107
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.21
Mean single sequence MFE -36.48
Consensus MFE -26.00
Energy contribution -26.64
Covariance contribution 0.64
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.71
SVM decision value 0.00
SVM RNA-class probability 0.535495
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293004 103 + 23771897
GCUGACCA-----------------GAUCGAGAUCUCAGUUCCCCGUCUCCAGCUGCUCCUCCAUUUGCAGACGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUUCCAGCUUG
((((...(-----------------(((.(.((.......)).).)))).)))).((.....((((((((.....))))))))...((((((((...((....))..))))))))))... ( -28.40)
>DroSec_CAF1 18932 103 + 1
GCUGACCA-----------------GAUCGAGAUCUCGGUCCACCGUCUCCAGCUGCUCCUCCAUUUGGAGUCGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUUCCAGCUUG
((((((((-----------------(((....)))).))))(((((.((((((.((......)).)))))).)))))..........(((((((...((....))..))))))))))... ( -37.90)
>DroSim_CAF1 14466 103 + 1
GCUGACCA-----------------GAUCGAGAUCUCGGUCCACCGUCUCCAGCUGCUCCUCCAUUUGGAGUCGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUUCCAGCUUG
((((((((-----------------(((....)))).))))(((((.((((((.((......)).)))))).)))))..........(((((((...((....))..))))))))))... ( -37.90)
>DroEre_CAF1 14806 117 + 1
GCUGACCAGGCCGAGACUCGUUCCAGAUCGAGAUCUCAGUCC-CCGUCUCCAGCUGCUCCUCCAUUUGGAGUUGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUU-CAGCUU-
(((((...(((.((((((((........)))).)))).)))(-((((...((..(((.(((((....)))...)).)))..))...(((.........)))..)))))...)-))))..- ( -37.50)
>DroYak_CAF1 14326 117 + 1
GCUGACCAGACCGAGACUCGUUCCAGAUCGAGAUCUCGUUGC-CCGUCUCCAGCUGCUCCUCCAUUUGGAGUUGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUU-CAGCUA-
((((((((...(((((((((........)))).)))))((((-(((.((((((.((......)).)))))).))).))))......)))......(((((......))))))-))))..- ( -40.70)
>consensus
GCUGACCA_________________GAUCGAGAUCUCGGUCC_CCGUCUCCAGCUGCUCCUCCAUUUGGAGUCGGUGCAAAUGAAAUGGAAAACGAAGCCAAAGCGGGUUUUCCAGCUUG
((((.(((.................((((((....))))))..(((.((((((.((......)).)))))).)))...........))).....((((((......)))))).))))... (-26.00 = -26.64 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,293,004 – 8,293,107
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.21
Mean single sequence MFE -40.02
Consensus MFE -27.53
Energy contribution -27.29
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.776574
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293004 103 - 23771897
CAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCGUCUGCAAAUGGAGGAGCAGCUGGAGACGGGGAACUGAGAUCUCGAUC-----------------UGGUCAGC
...((((.....(((((((..(((..((..(((..((((((((((.....))))))))))))))))))..))).))))..(((.((((....)))-----------------)))))))) ( -37.80)
>DroSec_CAF1 18932 103 - 1
CAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCGACUCCAAAUGGAGGAGCAGCUGGAGACGGUGGACCGAGAUCUCGAUC-----------------UGGUCAGC
...((((((((((..((....))...)))))))..........(((((.(((((..((......))..))))).)))))((((.((((....)))-----------------)))))))) ( -37.20)
>DroSim_CAF1 14466 103 - 1
CAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCGACUCCAAAUGGAGGAGCAGCUGGAGACGGUGGACCGAGAUCUCGAUC-----------------UGGUCAGC
...((((((((((..((....))...)))))))..........(((((.(((((..((......))..))))).)))))((((.((((....)))-----------------)))))))) ( -37.20)
>DroEre_CAF1 14806 117 - 1
-AAGCUG-AAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCAACUCCAAAUGGAGGAGCAGCUGGAGACGG-GGACUGAGAUCUCGAUCUGGAACGAGUCUCGGCCUGGUCAGC
-..((((-(...(((((((..(((.(.((((((((((...(((...)))....))))))))))).)))..))).)))-)..((((((.((((........)))))))))).....))))) ( -44.50)
>DroYak_CAF1 14326 117 - 1
-UAGCUG-AAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCAACUCCAAAUGGAGGAGCAGCUGGAGACGG-GCAACGAGAUCUCGAUCUGGAACGAGUCUCGGUCUGGUCAGC
-..((((-(...(((((((..(((.(.((((((((((...(((...)))....))))))))))).)))..))).)))-)...(((((.((((........)))))))))......))))) ( -43.40)
>consensus
CAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAUUUGCACCGACUCCAAAUGGAGGAGCAGCUGGAGACGG_GGACCGAGAUCUCGAUC_________________UGGUCAGC
...((((.....(((((((..(((.(.((((((((((................))))))))))).)))..))).))).)...(((....)))........................)))) (-27.53 = -27.29 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,293,067 – 8,293,187
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.29
Mean single sequence MFE -29.96
Consensus MFE -25.40
Energy contribution -25.64
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -1.23
Structure conservation index 0.85
SVM decision value -0.04
SVM RNA-class probability 0.514723
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8293067 120 - 23771897
AAAAUUUCGCCCAGUGCACAUGUGUGCUUUUCUAUGGUCGCUUAUGUAAGGCAACCACCGUGCCGGCUUCUGCCCCAUUUCAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
........(.(((..((((....)))).......))).)((((......((((.......))))(((....))).......))))((((((((..((....))...))))))))...... ( -30.40)
>DroSec_CAF1 18995 120 - 1
ACAAUUUCGCCCAGUGCACAUGUGUGCUUUUCUAUGGUCGCUUAUGUAAGGCAACCACUGUGCCGGCUUCUGCCCCAUUUCAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
........((.((((((((....))))........(((.((((.....)))).))))))).)).(((....)))...........((((((((..((....))...))))))))...... ( -32.90)
>DroSim_CAF1 14529 120 - 1
ACAAUUUCGCCCAGUGUACAUGUGUGCUUUUCUAUGGUCGCUUAUGUAAGGCAACCACUGUGCCGGCUUCUGCCCCAUUUCAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
........((.(((((((((((.(((((.......)).))).)))))).(....)))))).)).(((....)))...........((((((((..((....))...))))))))...... ( -31.10)
>DroEre_CAF1 14885 113 - 1
-----UUCGCCAAGUGCGCAUGUGUGCUUUUCUAUGAACGGUUAUGUAAGGCAUCCACUGUGCCGGCUUCUGCCCCAUUU-AAGCUG-AAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
-----...((((((.(((((....)))...........(((((......(((((.....)))))(((....)))......-.)))))-.......))))))))................. ( -27.70)
>DroYak_CAF1 14405 113 - 1
-----UUCGCCAAGUGCGCAUGUGUGCUUUUCUAUGGUCGGUUAUGUAAGGCAUCCACUGUGCCGACUUCUGCCCCAUUU-UAGCUG-AAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
-----...((((((.(((.......(((.....((((..(((.......(((((.....))))).......)))))))..-.)))..-......)))))))))................. ( -27.70)
>consensus
A_AAUUUCGCCCAGUGCACAUGUGUGCUUUUCUAUGGUCGCUUAUGUAAGGCAACCACUGUGCCGGCUUCUGCCCCAUUUCAAGCUGGAAAACCCGCUUUGGCUUCGUUUUCCAUUUCAU
........((...(.(((((((..((((((..(((((....))))).))))))..)).))))))(((....))).........))((((((((..((....))...))))))))...... (-25.40 = -25.64 +   0.24)

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 10:44:47 2006