Locus 1337

Sequence ID 3L_DroMel_CAF1
Location 3,876,710 – 3,876,876
Length 166
Max. P 0.999056
window2085 window2086 window2087 window2088

overview

Window 5

Location 3,876,710 – 3,876,800
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 77.70
Mean single sequence MFE -38.08
Consensus MFE -28.70
Energy contribution -28.98
Covariance contribution 0.28
Combinations/Pair 1.27
Mean z-score -1.40
Structure conservation index 0.75
SVM decision value 0.40
SVM RNA-class probability 0.722143
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3876710 90 + 23771897
GCGCAAGGAGGCGUCGAAGGCGGCAAUGGAACGCUCGCCCCCGCCUAUCCCCGGAGAAGUCCAGGGGCGGAGCGAAGGAGACGCUCCUGC
..(((.((((.((((...((((((........)).))))(((((((..(((.(((....))).)))..)).)))..)).))))))))))) ( -41.10)
>DroSec_CAF1 8770 88 + 1
GCGCAAGGAGGCGUCGAAGGCGGCAAUGGAACGCUCGCCCCCGCCCACCCCCGG--UAGUCCAGGGGCGGAGCGAAGGAGACGCUCCUGC
..(((.((((.((((...((((((........)).))))(((((((.((((.((--....)).)))).)).)))..)).))))))))))) ( -44.30)
>DroEre_CAF1 5301 88 + 1
GCGCAAGGAGGCGUCGAAGGCGGCAAUGGAACGCUCGCCCCCGCCCACCACCGG--AGGUCCGGGGGCGGAGCGAAGGAGACGCUCCUGC
..(((.((((.((((...((((((........)).))))(((((((.((.((((--....)))).)).)).)))..)).))))))))))) ( -44.00)
>DroYak_CAF1 345 88 + 1
GCGCAAGGAGGCGUCGAAGGCGGCAAUGGAACGCUCGCCCCCGCCCACCACUGG--AAAUCCAGGAGCGGAGCGAAGGAGACGCUCCUGC
..(((.((((.((((...((((((........)).))))(((((((.(..((((--....))))..).)).)))..)).))))))))))) ( -40.30)
>DroMoj_CAF1 342 71 + 1
GCGUUUGCACCCAUCGAAGACGGCAAUUCGACGCGCGCCCCCGCCCACG------------------AAGAGCGUAGG-AAUGGGCAAAC
((((((((...(......)...)))....)))))..((((...((.(((------------------.....))).))-...)))).... ( -20.70)
>consensus
GCGCAAGGAGGCGUCGAAGGCGGCAAUGGAACGCUCGCCCCCGCCCACCACCGG__AAGUCCAGGGGCGGAGCGAAGGAGACGCUCCUGC
..(((.((.((((((...((((((........)).))))(((((((.((.((((......)))).)).)).)))..)).))))))))))) (-28.70 = -28.98 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,876,710 – 3,876,800
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 77.70
Mean single sequence MFE -47.36
Consensus MFE -41.10
Energy contribution -39.90
Covariance contribution -1.20
Combinations/Pair 1.35
Mean z-score -3.53
Structure conservation index 0.87
SVM decision value 3.35
SVM RNA-class probability 0.999056
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3876710 90 - 23771897
GCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUUCUCCGGGGAUAGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCUUGCGC
(((((((((((......(((...((((.(((....)))))))...)))(((((((.(((......)))))))))))))).)))).))).. ( -46.70)
>DroSec_CAF1 8770 88 - 1
GCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUA--CCGGGGGUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCUUGCGC
(((((((((((......((.((((((((((....--))))))))))))(((((((.(((......)))))))))))))).)))).))).. ( -56.30)
>DroEre_CAF1 5301 88 - 1
GCAGGAGCGUCUCCUUCGCUCCGCCCCCGGACCU--CCGGUGGUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCUUGCGC
(((((((((((......((.(((((.((((....--)))).)))))))(((((((.(((......)))))))))))))).)))).))).. ( -52.40)
>DroYak_CAF1 345 88 - 1
GCAGGAGCGUCUCCUUCGCUCCGCUCCUGGAUUU--CCAGUGGUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCUUGCGC
(((((((((((......((.((((..((((....--))))..))))))(((((((.(((......)))))))))))))).)))).))).. ( -49.70)
>DroMoj_CAF1 342 71 - 1
GUUUGCCCAUU-CCUACGCUCUU------------------CGUGGGCGGGGGCGCGCGUCGAAUUGCCGUCUUCGAUGGGUGCAAACGC
((((((((...-((((((.....------------------))))))((((((((.(((......)))))))))))...)).)))))).. ( -31.70)
>consensus
GCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUU__CCGGGGGUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCUUGCGC
(((((.(((((......((.(((((.((((......)))).)))))))(((((((.(((......)))))))))))))))...))))).. (-41.10 = -39.90 +  -1.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,876,733 – 3,876,839
Length 106
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.52
Mean single sequence MFE -49.92
Consensus MFE -37.73
Energy contribution -38.57
Covariance contribution 0.84
Combinations/Pair 1.25
Mean z-score -2.63
Structure conservation index 0.76
SVM decision value 1.16
SVM RNA-class probability 0.923894
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3876733 106 - 23771897
GUUUCCGAU-CACGAAACUCAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUUCUCCGGGGAUAGGCGGGGGCGAGCGUUCCAUUG
(((((....-...))))).....(((((.(((...))))))))((((((((.((((((((...((((.(((....)))))))...)))))))).)).)))))).... ( -50.40)
>DroVir_CAF1 342 87 - 1
GUUCCA-AUGUUAGGAGCUUGAUUGCAGACGCAUUGCGCCGUUGGCUCAUC-CAUACGCUCUU------------------CGUGGGUGGGGGCGUGCGCUACAUUG
(((((.-......))))).....(((....)))..((((((((..((((((-(((........------------------.))))))))))))).))))....... ( -28.60)
>DroSec_CAF1 8793 104 - 1
GUUUCCGAU-CACGAAACUGAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUA--CCGGGGGUGGGCGGGGGCGAGCGUUCCAUUG
(((((....-...))))).....(((((.(((...))))))))((((((((.(((((((.((((((((((....--))))))))))))))))).)).)))))).... ( -60.00)
>DroSim_CAF1 9683 104 - 1
GUUUCCGAU-CACGAAACUCAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUU--CCGGGGGUGGGCGGGGGCGAGCGUUCUAUUG
(((((....-...))))).....(((((.(((...))))))))((((((((.(((((((.((((((((((....--))))))))))))))))).)).)))))).... ( -58.40)
>DroEre_CAF1 5324 104 - 1
GUUCCCGAU-CACGGAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCCGGACCU--CCGGUGGUGGGCGGGGGCGAGCGUUCCAUUG
(((((....-...))))).....(((.(.(((...)))).)))((((((((.(((((((.(((((.((((....--)))).)))))))))))).)).)))))).... ( -52.40)
>DroYak_CAF1 368 104 - 1
GUUCCCGAU-CACGGAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCUCCUGGAUUU--CCAGUGGUGGGCGGGGGCGAGCGUUCCAUUG
(((((....-...))))).....(((.(.(((...)))).)))((((((((.(((((((.((((..((((....--))))..))))))))))).)).)))))).... ( -49.70)
>consensus
GUUCCCGAU_CACGAAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUU__CCGGGGGUGGGCGGGGGCGAGCGUUCCAUUG
(((((........))))).....(((.(.(((...)))).)))((((((((.(((((((.(((((.((((......)))).)))))))))))).)).)))))).... (-37.73 = -38.57 +   0.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,876,763 – 3,876,876
Length 113
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 81.94
Mean single sequence MFE -39.60
Consensus MFE -30.09
Energy contribution -30.62
Covariance contribution 0.53
Combinations/Pair 1.19
Mean z-score -1.52
Structure conservation index 0.76
SVM decision value 0.27
SVM RNA-class probability 0.661002
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3876763 113 - 23771897
AGGAGAAGAGCUUUAAAAAGGGUGCUCGUCCUGGCACGUUUCCGAUCACGAAACUCAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUUCUC
..(((((((((............))))((((.(((..(((((.......))))).....(((((.(((...))))))))((((((.......)))))))))...))))))))) ( -45.20)
>DroSec_CAF1 8823 111 - 1
UCGGAAAGAGCUUUAAAAAGGGUGCUCGUCCUGGCACGUUUCCGAUCACGAAACUGAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUA--C
.......((((............))))((((.(((..(((((.......))))).....(((((.(((...))))))))((((((.......)))))))))...))))..--. ( -41.60)
>DroSim_CAF1 9713 111 - 1
UCGGAAAGAGCUUUAAAAAGGGUGCUCGUCCUGGCACGUUUCCGAUCACGAAACUCAAGUGCGGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUU--C
.......((((............))))((((.(((..(((((.......))))).....(((((.(((...))))))))((((((.......)))))))))...))))..--. ( -41.60)
>DroEre_CAF1 5354 110 - 1
CCACAUAGAGUUUUAA-AAGGGCGCUCGUCCUGGCACGUUCCCGAUCACGGAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCCGGACCU--C
((..............-...(((((.((((...(((((((((.......)))))....)))).))))....)))))((.((((((.......))))))))....))....--. ( -39.00)
>DroYak_CAF1 398 110 - 1
GAAUGGAGAGCUUUAA-AAGGGCGCUCGUCCUGGCACGUUCCCGAUCACGGAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCUCCUGGAUUU--C
....((.((((.....-...(((((.((((...(((((((((.......)))))....)))).))))....)))))...((((((.......))))))))))))......--. ( -42.80)
>DroAna_CAF1 29618 93 - 1
UUGGCAAAUGUGUUAA-AAGGGUGCUCGUCUUGGCGCGUU--CGAUCGCUGAACAAAAGUGCAGACGCAUUGCGCCGCAGGACCAUCUCAUUUUCU-----------------
((((((....))))))-..(((((...(((((((((((((--((.....)))))...(((((....)))))))))))..)))))))))........----------------- ( -27.40)
>consensus
UCGGAAAGAGCUUUAA_AAGGGUGCUCGUCCUGGCACGUUUCCGAUCACGAAACUCAAGUGCAGACGCAUUGCGCCGCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUU__C
....................(((((.(((((..(((((((((.......)))))....)))))))))....)))))((.((((((.......))))))))............. (-30.09 = -30.62 +   0.53)

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 10:05:07 2006