Locus 8818

Sequence ID 3R_DroMel_CAF1
Location 23,602,287 – 23,602,412
Length 125
Max. P 0.787579
window14162 window14163

overview

Window 2

Location 23,602,287 – 23,602,398
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 80.93
Mean single sequence MFE -25.53
Consensus MFE -17.54
Energy contribution -18.98
Covariance contribution 1.44
Combinations/Pair 1.23
Mean z-score -1.85
Structure conservation index 0.69
SVM decision value 0.58
SVM RNA-class probability 0.787579
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23602287 111 - 27905053
UUUUAUUUUGAGUAUUUGUACUUAAACAUAUUUAAAAUGAAUUUCUUUGCUUUCGAUGCCAAUAAUUGGGAGAAGGCAAAAGAACUUGGGUAAAUAUGGUCCAAUCCUCGU
......((((((((....))))))))((((((((...(.((.((((((((((((....(((.....)))..)))))).)))))).)).).))))))))............. ( -26.20)
>DroSec_CAF1 63533 111 - 1
UUUUAUUUUGAGUAUUUGUGCUUUAACAUAUUUUAAAGGAAUUUCUUUGCUUUCGAUGGCAAUAAUUGGGAGAAGGCAAAGAAACUUGGGUAAAUAAGGUCCAAUCCUCGU
.........(((...(((..(((((...((((...(((...(((((((((((((.................)))))))))))))))).))))..)))))..)))..))).. ( -24.23)
>DroEre_CAF1 65322 111 - 1
UAUUAUCUUGAGUAUUUGUCUCUAAAUAUAUUUUAAAGGAAUUUCCUUGCUUUCGAUGCCAAUAAUUGGAAGAAGGCAAGGGAACUUGGGUAAAUACGGUCCAAACCUCGU
...........(((((((.(((((((.....))))......(((((((((((((....(((.....)))..)))))))))))))...))))))))))(((....))).... ( -29.90)
>DroYak_CAF1 69198 100 - 1
UUUUAUCUUAAGUGUUUG-----------AAUUGAGAUGAAGUUCUUUGCUUUCGAUGUCAAUAAUUGGCAGAAGCCAAAGGAUCUUUAGUAAAUAAAGUGCAAACAUCGU
(((((((((((.......-----------..)))))))))))...........((((((......(((((....))))).(.(.(((((.....)))))).)..)))))). ( -21.80)
>consensus
UUUUAUCUUGAGUAUUUGU_CUUAAACAUAUUUUAAAGGAAUUUCUUUGCUUUCGAUGCCAAUAAUUGGGAGAAGGCAAAGGAACUUGGGUAAAUAAGGUCCAAACCUCGU
.((((((((((((((............))))))))))))))(((((((((((((....(((.....)))..)))))))))))))........................... (-17.54 = -18.98 +   1.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,602,318 – 23,602,412
Length 94
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 79.09
Mean single sequence MFE -20.90
Consensus MFE -11.12
Energy contribution -12.57
Covariance contribution 1.45
Combinations/Pair 1.16
Mean z-score -2.42
Structure conservation index 0.53
SVM decision value 0.09
SVM RNA-class probability 0.580483
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23602318 94 - 27905053
-UAUAUUUGCAA-UCAUUUUAUUUUGAGUAUUUGUACUUAAACAUAUUUAAAAUGAAUUUCUUUGCUUUCGAUGCCAAUAAUUGGGAGAAGGCAAA
-...........-((((((((.((((((((....))))))))......))))))))......((((((((....(((.....)))..)))))))). ( -20.60)
>DroSec_CAF1 63564 95 - 1
-UAUAUUUACAACUCAUUUUAUUUUGAGUAUUUGUGCUUUAACAUAUUUUAAAGGAAUUUCUUUGCUUUCGAUGGCAAUAAUUGGGAGAAGGCAAA
-..........(((((........))))).....((((((.........((((((....))))))((..((((.......))))..)))))))).. ( -17.90)
>DroYak_CAF1 69229 85 - 1
AGAUAUUUCCAAGGCAUUUUAUCUUAAGUGUUUG-----------AAUUGAGAUGAAGUUCUUUGCUUUCGAUGUCAAUAAUUGGCAGAAGCCAAA
.((((((..(((((.((((((((((((.......-----------..)))))))))))).))))).....)))))).....(((((....))))). ( -24.20)
>consensus
_UAUAUUUACAA_UCAUUUUAUUUUGAGUAUUUGU_CUU_AACAUAUUUAAAAUGAAUUUCUUUGCUUUCGAUGCCAAUAAUUGGGAGAAGGCAAA
.................((((((((((((((............)))))))))))))).....((((((((....(((.....)))..)))))))). (-11.12 = -12.57 +   1.45)

alignment

Postscript

secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:30 2006