Locus 2525

Sequence ID 3L_DroMel_CAF1
Location 7,080,340 – 7,080,439
Length 99
Max. P 0.954186
window3920 window3921

overview

Window 0

Location 7,080,340 – 7,080,439
Length 99
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 91.48
Mean single sequence MFE -32.05
Consensus MFE -26.23
Energy contribution -27.47
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 0.82
SVM decision value 1.44
SVM RNA-class probability 0.954186
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7080340 99 + 23771897
CUGGGCACCUGUAAAUGCGGCCAAACUUGUUGCAUG-------UUUUGGGUGCUGUCAUAAGUGCAUAAGU-GCAAGCCUUU-G-AACAUAUUUAUGCACUUUGGUGGC
...((((((((...(((((((.......))))))).-------...))))))))(((((((((((((((((-(....(....-)-....)))))))))))))..))))) ( -35.20)
>DroSec_CAF1 92826 99 + 1
CUGGGCACCUGUAAGUGCGGCCAAACUUGUUGCAUG-------UUUUGGGUGCUGUCAUAAAUGCAUAAGU-GCAAGCCUUU-G-AACAUAUUUAUGCACUUUGGUGGC
...((((((((...(((((((.......))))))).-------...))))))))(((((...(((((((((-(....(....-)-....)))))))))).....))))) ( -30.50)
>DroSim_CAF1 125448 99 + 1
CUGGGCACCUGUAAAUGCGGCCAAACUUGUUGCAUG-------UUUUGGGUGCUGUCAUAAGUGCAUAAGU-GCAAGCCUUU-G-AACAUAUUUAUGCACUUUGGUGGC
...((((((((...(((((((.......))))))).-------...))))))))(((((((((((((((((-(....(....-)-....)))))))))))))..))))) ( -35.20)
>DroEre_CAF1 108863 106 + 1
CGGGCCACCUGUAAAUGCGGCCAAACUUGUUGCAUGAGCUGAGAUUGGGGUGCUGUCAUAAGUGCAUAAG---CAAGCCUUUGAAAACAUAUUUAUGCACUUUGGUGGC
...((((((.......(((.((...(((...((....)).)))....)).)))......(((((((((((---..................))))))))))).)))))) ( -29.07)
>DroYak_CAF1 108105 101 + 1
CUGGGCACCUGUAAAUGCGGCCAAACUUUUUGCAUG-------UUUGGGGUGCUGUCAUAAGUGCAUAAGCAGCAAGCCUUUUG-AACAUAUUUAUGCACUUUGGUGGC
...(((((((((....))).((((((.........)-------)))))))))))((((((((((((((((.(.((((...))))-....).)))))))))))..))))) ( -30.30)
>consensus
CUGGGCACCUGUAAAUGCGGCCAAACUUGUUGCAUG_______UUUUGGGUGCUGUCAUAAGUGCAUAAGU_GCAAGCCUUU_G_AACAUAUUUAUGCACUUUGGUGGC
...((((((((...(((((((.......)))))))...........))))))))(((((((((((((((((...................))))))))))))..))))) (-26.23 = -27.47 +   1.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,080,340 – 7,080,439
Length 99
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 91.48
Mean single sequence MFE -24.62
Consensus MFE -18.65
Energy contribution -18.53
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.55
Structure conservation index 0.76
SVM decision value -0.03
SVM RNA-class probability 0.516219
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7080340 99 - 23771897
GCCACCAAAGUGCAUAAAUAUGUU-C-AAAGGCUUGC-ACUUAUGCACUUAUGACAGCACCCAAAA-------CAUGCAACAAGUUUGGCCGCAUUUACAGGUGCCCAG
..((((.((((((((((....((.-(-((....))).-))))))))))))......((..(((((.-------..(......).)))))..)).......))))..... ( -22.20)
>DroSec_CAF1 92826 99 - 1
GCCACCAAAGUGCAUAAAUAUGUU-C-AAAGGCUUGC-ACUUAUGCAUUUAUGACAGCACCCAAAA-------CAUGCAACAAGUUUGGCCGCACUUACAGGUGCCCAG
..((((.(((((((((....))).-.-...((((...-((((.(((((((.((........)).))-------.)))))..))))..))))))))))...))))..... ( -22.20)
>DroSim_CAF1 125448 99 - 1
GCCACCAAAGUGCAUAAAUAUGUU-C-AAAGGCUUGC-ACUUAUGCACUUAUGACAGCACCCAAAA-------CAUGCAACAAGUUUGGCCGCAUUUACAGGUGCCCAG
..((((.((((((((((....((.-(-((....))).-))))))))))))......((..(((((.-------..(......).)))))..)).......))))..... ( -22.20)
>DroEre_CAF1 108863 106 - 1
GCCACCAAAGUGCAUAAAUAUGUUUUCAAAGGCUUG---CUUAUGCACUUAUGACAGCACCCCAAUCUCAGCUCAUGCAACAAGUUUGGCCGCAUUUACAGGUGGCCCG
((((((.((((((((((.((.((((....)))).))---.))))))))))......((...((((.((..((....))....)).))))..)).......))))))... ( -32.00)
>DroYak_CAF1 108105 101 - 1
GCCACCAAAGUGCAUAAAUAUGUU-CAAAAGGCUUGCUGCUUAUGCACUUAUGACAGCACCCCAAA-------CAUGCAAAAAGUUUGGCCGCAUUUACAGGUGCCCAG
..((((.(((((((((........-.....(((.....))))))))))))......((...(((((-------(.........))))))..)).......))))..... ( -24.51)
>consensus
GCCACCAAAGUGCAUAAAUAUGUU_C_AAAGGCUUGC_ACUUAUGCACUUAUGACAGCACCCAAAA_______CAUGCAACAAGUUUGGCCGCAUUUACAGGUGCCCAG
((((.((((((((((((....(((......))).......)))))))))).))...(((................)))........)))).(((((....))))).... (-18.65 = -18.53 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:51 2006