Locus 8240

Sequence ID 3R_DroMel_CAF1
Location 22,070,456 – 22,070,569
Length 113
Max. P 0.993867
window13285 window13286

overview

Window 5

Location 22,070,456 – 22,070,569
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.26
Mean single sequence MFE -26.94
Consensus MFE -24.47
Energy contribution -24.87
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.91
SVM decision value 2.17
SVM RNA-class probability 0.989564
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22070456 113 + 27905053
GACCAUU-UACUUUUUAUUUCCAGAUGUGUCGCAAGAUUUGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCA--CAUCUCCAUUGCAGUC----GGCCGCAAAUGAAAAUAA
(((((((-(.............))))).))).....((((((..(((..........(((((((((.....((((((...--))))))))))))))))----))..))))))........ ( -26.02)
>DroSec_CAF1 62504 116 + 1
GACCAUUUUACUCUUUAUUUCCAGAUGUGUCGCAAGAUUUGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCACACAUCUCCAUUGCAUUC----GGCCGCAAAUGAAAAUAA
((((((((..............))))).))).....((((((..(((((..........)))(((((((..((((((.....))))))..))))))).----))..))))))........ ( -28.24)
>DroSim_CAF1 55492 114 + 1
GACCAUUUUACUCUUUAUUUCCAGAUGUGUCGCAAGAUUUGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCA--CAUCUCCAUUGCAGUC----GGCCGCAAAUGAAAAUAA
((((((((..............))))).))).....((((((..(((..........(((((((((.....((((((...--))))))))))))))))----))..))))))........ ( -25.74)
>DroEre_CAF1 57008 112 + 1
GACCAUU-UACUUUUUAUUUCCAGAUGUGUCGCAAGAU-AGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCA--CAUCUCCAUUGCACUC----GGCCGCAAAUGAAAAUAA
.......-...(((((((((.......((((....)))-)((..(((((..........)))..(((((..((((((...--))))))..)))))...----))..)))))))))))... ( -25.90)
>DroYak_CAF1 64946 117 + 1
GACCAUU-UACUUUUUAUUUCCAGAUGUGUCGCAAGAUUUGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCA--CAUCUCUAUUGCAGUCGGUCGGCCGCAAAUGAAAAUAA
.......-......((((((.((..((((((....))...(((.(((((..........)))..(((((.(((((((...--))))))).)))))...))..)))))))..)).)))))) ( -28.80)
>consensus
GACCAUU_UACUUUUUAUUUCCAGAUGUGUCGCAAGAUUUGCUUCCGCAUUUUACUCAUUGCAAUGCAAAAGAGGUGCCA__CAUCUCCAUUGCAGUC____GGCCGCAAAUGAAAAUAA
(((((((................)))).))).....((((((..(((((..........)))..(((((..((((((.....))))))..))))).......))..))))))........ (-24.47 = -24.87 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,070,456 – 22,070,569
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.26
Mean single sequence MFE -32.74
Consensus MFE -28.24
Energy contribution -28.28
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.19
Structure conservation index 0.86
SVM decision value 2.43
SVM RNA-class probability 0.993867
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22070456 113 - 27905053
UUAUUUUCAUUUGCGGCC----GACUGCAAUGGAGAUG--UGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCAAAUCUUGCGACACAUCUGGAAAUAAAAAGUA-AAUGGUC
((((((((..((((((..----..))))))...(((((--(((((.......))).((((((.((......(((....)))..)))))))))))))))))))))))......-....... ( -32.90)
>DroSec_CAF1 62504 116 - 1
UUAUUUUCAUUUGCGGCC----GAAUGCAAUGGAGAUGUGUGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCAAAUCUUGCGACACAUCUGGAAAUAAAGAGUAAAAUGGUC
((((((((..(((((...----...)))))...((((((((.(((.(((..((((...)))).))).....(((....))).....))).)))))))))))))))).............. ( -35.60)
>DroSim_CAF1 55492 114 - 1
UUAUUUUCAUUUGCGGCC----GACUGCAAUGGAGAUG--UGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCAAAUCUUGCGACACAUCUGGAAAUAAAGAGUAAAAUGGUC
((((((((..((((((..----..))))))...(((((--(((((.......))).((((((.((......(((....)))..))))))))))))))))))))))).............. ( -32.90)
>DroEre_CAF1 57008 112 - 1
UUAUUUUCAUUUGCGGCC----GAGUGCAAUGGAGAUG--UGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCU-AUCUUGCGACACAUCUGGAAAUAAAAAGUA-AAUGGUC
((((((((..(((((...----...)))))...(((((--(((((.......))).((((((.((.......((....)).-.)))))))))))))))))))))))......-....... ( -28.90)
>DroYak_CAF1 64946 117 - 1
UUAUUUUCAUUUGCGGCCGACCGACUGCAAUAGAGAUG--UGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCAAAUCUUGCGACACAUCUGGAAAUAAAAAGUA-AAUGGUC
((((((((..((((((.(....).))))))...(((((--(((((.......))).((((((.((......(((....)))..)))))))))))))))))))))))......-....... ( -33.40)
>consensus
UUAUUUUCAUUUGCGGCC____GACUGCAAUGGAGAUG__UGGCACCUCUUUUGCAUUGCAAUGAGUAAAAUGCGGAAGCAAAUCUUGCGACACAUCUGGAAAUAAAAAGUA_AAUGGUC
(((((((((..((.(..........(((((.((((.((.....)).)))).)))))((((((.((......(((....)))..))))))))).))..))))))))).............. (-28.24 = -28.28 +   0.04)

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 13:06:33 2006