Locus 1818

Sequence ID 3L_DroMel_CAF1
Location 5,101,992 – 5,102,147
Length 155
Max. P 0.993595
window2836 window2837 window2838

overview

Window 6

Location 5,101,992 – 5,102,107
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.33
Mean single sequence MFE -34.08
Consensus MFE -30.05
Energy contribution -29.68
Covariance contribution -0.37
Combinations/Pair 1.09
Mean z-score -2.94
Structure conservation index 0.88
SVM decision value 2.41
SVM RNA-class probability 0.993595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5101992 115 + 23771897
CAACCGGUUCUGCAUUAAAAUGAUCUUGCUGAUCUUCUGGUGCAGCAGCAGCAGCAACUUCUUCUUCAUUUUGCCUCAAUUUGGCAAUAUGGACGAAGCAACCACA-----AUAUAGCCG
....(((((((((((((.((.((((.....)))))).))))))))..((....)).....(((((((((.(((((.......))))).))))).))))........-----....))))) ( -32.50)
>DroSec_CAF1 295033 109 + 1
CAACCGGUUCUGCAGCAAAAUGAUCUUGCUGAUCUUCUGGUGCAGC------AGCAACUUCUUCUUCGUUUUGCCUCAAUUUGGAAAUAUGGAAGAAGCAACCACA-----UUAUAGCCG
....((((((((((.((.((.((((.....)))))).)).))))).------.....((((((((..(((...((.......)).)))..))))))))........-----....))))) ( -28.70)
>DroSim_CAF1 316647 112 + 1
CAACCGGUUCUGCAGCAAAAUGAUCUUGCUGAUCUUCUGGUGCAGCA---GCAGCAACUUCUUCUUCAUUUUGCCUCAAUUUGGCAAUAUGGAAGAAGCAACCACA-----AUAUAGCCG
....((((((((((.((.((.((((.....)))))).)).)))))..---.......(((((((..(((.(((((.......))))).))))))))))........-----....))))) ( -33.80)
>DroYak_CAF1 307317 114 + 1
CAACCGGUUCUGCAGCAAAAUGAUCUUGCUGAUCUUCUGGUGCAGC------AGCAGCUUCUUCUUCGUUUUGCCUCAAUUUGGCAAUAUGAAAGAAGAAGCCACAUAGCCAUAUAGCCG
....((((((((((.((.((.((((.....)))))).)).))))).------....(((((((((((((.(((((.......))))).))).)))))))))).............))))) ( -41.30)
>consensus
CAACCGGUUCUGCAGCAAAAUGAUCUUGCUGAUCUUCUGGUGCAGC______AGCAACUUCUUCUUCAUUUUGCCUCAAUUUGGCAAUAUGGAAGAAGCAACCACA_____AUAUAGCCG
....((((((((((.((.((.((((.....)))))).)).)))))...............(((((((((.(((((.......))))).))))).)))).................))))) (-30.05 = -29.68 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,101,992 – 5,102,107
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.33
Mean single sequence MFE -37.58
Consensus MFE -32.44
Energy contribution -32.62
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -2.94
Structure conservation index 0.86
SVM decision value 2.24
SVM RNA-class probability 0.990969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5101992 115 - 23771897
CGGCUAUAU-----UGUGGUUGCUUCGUCCAUAUUGCCAAAUUGAGGCAAAAUGAAGAAGAAGUUGCUGCUGCUGCUGCACCAGAAGAUCAGCAAGAUCAUUUUAAUGCAGAACCGGUUG
(((......-----.(..((.(((((.(((((.(((((.......))))).)))..)).))))).))..).....(((((..((((((((.....)))).))))..)))))..))).... ( -34.30)
>DroSec_CAF1 295033 109 - 1
CGGCUAUAA-----UGUGGUUGCUUCUUCCAUAUUUCCAAAUUGAGGCAAAACGAAGAAGAAGUUGCU------GCUGCACCAGAAGAUCAGCAAGAUCAUUUUGCUGCAGAACCGGUUG
(((......-----.(..((.((((((((....(((((.......)).))).....)))))))).)).------.)((((.(((((((((.....)))).))))).))))...))).... ( -30.60)
>DroSim_CAF1 316647 112 - 1
CGGCUAUAU-----UGUGGUUGCUUCUUCCAUAUUGCCAAAUUGAGGCAAAAUGAAGAAGAAGUUGCUGC---UGCUGCACCAGAAGAUCAGCAAGAUCAUUUUGCUGCAGAACCGGUUG
(((......-----.(..((.(((((((((((.(((((.......))))).)))..)))))))).))..)---..(((((.(((((((((.....)))).))))).)))))..))).... ( -41.90)
>DroYak_CAF1 307317 114 - 1
CGGCUAUAUGGCUAUGUGGCUUCUUCUUUCAUAUUGCCAAAUUGAGGCAAAACGAAGAAGAAGCUGCU------GCUGCACCAGAAGAUCAGCAAGAUCAUUUUGCUGCAGAACCGGUUG
(((............(..(((((((((((....(((((.......)))))...)))))))))))..).------.(((((.(((((((((.....)))).))))).)))))..))).... ( -43.50)
>consensus
CGGCUAUAU_____UGUGGUUGCUUCUUCCAUAUUGCCAAAUUGAGGCAAAACGAAGAAGAAGUUGCU______GCUGCACCAGAAGAUCAGCAAGAUCAUUUUGCUGCAGAACCGGUUG
(((............(..(((.(((((((....(((((.......)))))...))))))).)))..)........(((((.(((((((((.....)))).))))).)))))..))).... (-32.44 = -32.62 +   0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,102,032 – 5,102,147
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.82
Mean single sequence MFE -26.85
Consensus MFE -19.11
Energy contribution -19.30
Covariance contribution 0.19
Combinations/Pair 1.12
Mean z-score -1.41
Structure conservation index 0.71
SVM decision value -0.04
SVM RNA-class probability 0.512705
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5102032 115 - 23771897
UUUGUUUUUAUCGUCUGAAAUUUACAAUUCAAUGUCAUGCCGGCUAUAU-----UGUGGUUGCUUCGUCCAUAUUGCCAAAUUGAGGCAAAAUGAAGAAGAAGUUGCUGCUGCUGCUGCA
...........(((.((((........)))))))...(((.(((.....-----.(..((.(((((.(((((.(((((.......))))).)))..)).))))).))..)....)))))) ( -25.40)
>DroSec_CAF1 295073 106 - 1
UU---UUUUAUCGUCUUAAAUUUACAAUUCAAUGUCAUGCCGGCUAUAA-----UGUGGUUGCUUCUUCCAUAUUUCCAAAUUGAGGCAAAACGAAGAAGAAGUUGCU------GCUGCA
((---((((.((((.........(((......)))..((((......((-----(((((.........)))))))..........))))..)))).))))))..(((.------...))) ( -16.89)
>DroSim_CAF1 316687 109 - 1
UU---UUUUAUCGUCUGAAAUUUACAAUUCAAUGUCAUGCCGGCUAUAU-----UGUGGUUGCUUCUUCCAUAUUGCCAAAUUGAGGCAAAAUGAAGAAGAAGUUGCUGC---UGCUGCA
..---......(((.((((........)))))))...(((.(((.....-----.(..((.(((((((((((.(((((.......))))).)))..)))))))).))..)---.)))))) ( -28.30)
>DroYak_CAF1 307357 106 - 1
--------UAUCGCCCGCAAUUUACAAUUCAAUGUCAUGCCGGCUAUAUGGCUAUGUGGCUUCUUCUUUCAUAUUGCCAAAUUGAGGCAAAACGAAGAAGAAGCUGCU------GCUGCA
--------....(((.(((....(((......)))..))).))).....(((...(..(((((((((((....(((((.......)))))...)))))))))))..).------)))... ( -36.80)
>consensus
UU___UUUUAUCGUCUGAAAUUUACAAUUCAAUGUCAUGCCGGCUAUAU_____UGUGGUUGCUUCUUCCAUAUUGCCAAAUUGAGGCAAAACGAAGAAGAAGUUGCU______GCUGCA
........................................((((((((......))))))))(((((((....(((((.......)))))...)))))))..((.((.......)).)). (-19.11 = -19.30 +   0.19)

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 10:17:31 2006