Locus 4892

Sequence ID 3R_DroMel_CAF1
Location 12,865,728 – 12,865,875
Length 147
Max. P 0.782056
window8010 window8011

overview

Window 0

Location 12,865,728 – 12,865,847
Length 119
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.21
Mean single sequence MFE -34.69
Consensus MFE -22.28
Energy contribution -23.53
Covariance contribution 1.25
Combinations/Pair 1.29
Mean z-score -1.85
Structure conservation index 0.64
SVM decision value 0.56
SVM RNA-class probability 0.782056
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12865728 119 - 27905053
GUUUUUUCAAAAUUAAGUGGUAAUUAUGCACCGAAUACCAUUGUAUAUGGGGUCGGAGCCUCGCCCCGAGGCCUCUGAAUAUAUCACGAUGUCCGAGGCCAUGUGUCCACGUAACCUGA
................((((....(((((..((.....(((((((((((...(((((((((((...))))).)))))).))))).))))))..))..).))))...))))......... ( -33.70)
>DroSec_CAF1 35435 119 - 1
UUUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGUAUAUGGCGUCGGAGCCUCGACCCGAGGCCUCUGAAUAUAUCACGAUGUCCGAGGUCAUGUGUCCACGUAACCUGA
................((((...(((((.(((......(((((((((((...(((((((((((...))))).)))))).))))).)))))).....))))))))..))))......... ( -38.70)
>DroSim_CAF1 36109 119 - 1
GUUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGUAUAUGGCGUCGGAGCCUCGACCCGAGGCCUCUGAAUAUAUCACGAUGUCCGAAGUCAUGUGUCCACGUAACCUAA
................((((...(((((.((.......(((((((((((...(((((((((((...))))).)))))).))))).))))))......)))))))..))))......... ( -34.12)
>DroEre_CAF1 35234 119 - 1
UUUUCUUCCAAAUUAGGUGGUGGAUAUGCAUAGAAUACCAUUGCAUAUGGUGUCGGAGCCUUGUCCAGAGGCCUCUGAAUACAUCACGAUGUCCGGGGUCAUGUGUCCACGUAACCUGA
............((((((.((((((..((((.((...((...((((.(((((((((((((((.....)))).))))))...)))))..))))...)).))))))))))))...)))))) ( -39.80)
>DroYak_CAF1 35485 118 - 1
-UUUUUUCCAAAUUAAGUGGUGAAUAUGCAUAGAAUACCAUUGCAUAUGGUGUCGGAGCCGUGCCCAGAGGCCUCUGAAUACAUCACGAUGUCCGGGGUCAUGUGUCCACGUAACCUGA
-...............((((((.(((((((...........)))))))....((((((((.........)).))))))...))))))........((((.((((....)))).)))).. ( -31.00)
>DroAna_CAF1 36628 118 - 1
-UAAAUUGCAAUUUCUUAUGAAAUUAUGCAUCGAAUUCCUCUGCAUCUUAUGGAUGAUCCUCAUCCCGGGGCUCCAGAAUGCGCCACAAUGUCAAUGGUCUUGACUCCGCGCAAUUUAA
-((((((((((((((....))))))..((.((((...((..(((((.....(((((.....))))).((.((........)).))...))).))..))..))))....)))))))))). ( -30.80)
>consensus
_UUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGCAUAUGGUGUCGGAGCCUCGACCCGAGGCCUCUGAAUACAUCACGAUGUCCGAGGUCAUGUGUCCACGUAACCUGA
................((((((.(((((((...........)))))))....((((((((((.....)))).))))))...))))))........((((.((((....)))).)))).. (-22.28 = -23.53 +   1.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,865,768 – 12,865,875
Length 107
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 76.43
Mean single sequence MFE -28.23
Consensus MFE -17.00
Energy contribution -17.29
Covariance contribution 0.29
Combinations/Pair 1.50
Mean z-score -1.40
Structure conservation index 0.60
SVM decision value 0.08
SVM RNA-class probability 0.573943
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12865768 107 - 27905053
CGAGAUCUU-CAAAACACGCUUUGAUGAG-GUUUUUUCAAAAUUAAGUGGUAAUUAUGCACCGAAUACCAUUGUAUAUGGGGUCGGAGCCUCGCCCCGAGGCCUCUGAA
..(((((((-((((......)))))..))-))))(..((......(((((((.((.......)).))))))).....))..)(((((((((((...))))).)))))). ( -26.90)
>DroSec_CAF1 35475 107 - 1
CGAGAUCUU-AAAAUCACGCUUUGAGGAG-UUUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGUAUAUGGCGUCGGAGCCUCGACCCGAGGCCUCUGAA
.(((.....-...(((((..((((((((.-...)))))))).....))))).........((((...((((.....))))..)))).((((((...))))))))).... ( -28.10)
>DroSim_CAF1 36149 107 - 1
CGAGAUCUU-AAAAUCACGCUUUGAGGAG-GUUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGUAUAUGGCGUCGGAGCCUCGACCCGAGGCCUCUGAA
.(((.....-...(((((..((((((((.-...)))))))).....))))).........((((...((((.....))))..)))).((((((...))))))))).... ( -28.10)
>DroEre_CAF1 35274 109 - 1
CGAGAGCUUCAAAAUCGCAUUUUUAAGAAGUUUUCUUCCAAAUUAGGUGGUGGAUAUGCAUAGAAUACCAUUGCAUAUGGUGUCGGAGCCUUGUCCAGAGGCCUCUGAA
.(((.(((((...(((((........((((....))))........)))))(((((.((...((.((((((.....))))))))...))..))))).)))))))).... ( -33.09)
>DroYak_CAF1 35525 107 - 1
CGAGAGCUUCAAAAAUACGCUUUUAAGAG--UUUUUUCCAAAUUAAGUGGUGAAUAUGCAUAGAAUACCAUUGCAUAUGGUGUCGGAGCCGUGCCCAGAGGCCUCUGAA
.(((.(((((.......(((((....(((--....)))......)))))....(((((((...........)))))))((((.((....))))))..)))))))).... ( -25.40)
>DroAna_CAF1 36668 107 - 1
CUUUCGCUUCAAAACUGCAAUUGCAAGGA--UAAAUUGCAAUUUCUUAUGAAAUUAUGCAUCGAAUUCCUCUGCAUCUUAUGGAUGAUCCUCAUCCCGGGGCUCCAGAA
.....(((((...........((((((((--.....(((((((((....)))))..))))......)))).))))......(((((.....))))).)))))....... ( -27.80)
>consensus
CGAGAGCUU_AAAAUCACGCUUUGAAGAG__UUUUUUCAAAAUUAAGUGGUAAAUAUGCACCGAAUACCAUUGCAUAUGGUGUCGGAGCCUCGACCCGAGGCCUCUGAA
.................(((((((((((.....))))))))....(((((((.............))))))).......)))((((((((((.....)))).)))))). (-17.00 = -17.29 +   0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:24 2006