Locus 1869

Sequence ID 3R_DroMel_CAF1
Location 5,363,758 – 5,363,913
Length 155
Max. P 0.997495
window3072 window3073

overview

Window 2

Location 5,363,758 – 5,363,876
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -14.42
Consensus MFE -13.85
Energy contribution -13.85
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.96
SVM decision value 0.02
SVM RNA-class probability 0.543672
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5363758 118 - 27905053
UUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAGCAAAAGAAAAAAAAACCAACAAGAAAACCAAACAGAAACAAUGAUAAUGAUAUCCUAUGAGGGGAAAAAAAAG
..............(((.(((((((((.....))))))((....))...............................))).......((((....))))......))).......... ( -14.70)
>DroSec_CAF1 23212 107 - 1
UUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAGCAAAAGAAAAAAAA----A---CAAAACCAAACAAAAACAAUGAUAAAGAUAUCCUAUGAGGGAAAAAA----
((((..(((((..............)))))(((((.((((....)))))))))......----)---)))...........................((((....)))).....---- ( -14.44)
>DroSim_CAF1 22642 114 - 1
UUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAGCAAAAGAAAAAAAAAACAA---CAAAACCAAACAAAAACAAUGAUAAUGAUAUCCUAUGAGGGGAAAAA-AAG
((((..(((((..............)))))(((((.((((....)))))))))..........)---)))...........................((((.....))))....-... ( -14.54)
>DroEre_CAF1 23408 109 - 1
UUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAGCAAAAAACAAAACA----A----AAAAACAAACAAAAACAAUGAUAAUGAUAUCCUAUGAGGGGAAAAA-AAG
..............(((.((((((((....))))))((((....))))...........----.----....................................))))).....-... ( -14.00)
>consensus
UUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAGCAAAAGAAAAAAAA____A___CAAAACCAAACAAAAACAAUGAUAAUGAUAUCCUAUGAGGGGAAAAA_AAG
..............(((...((((((....))))))((((....)))).........................................................))).......... (-13.85 = -13.85 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,363,797 – 5,363,913
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.00
Mean single sequence MFE -16.36
Consensus MFE -15.06
Energy contribution -15.46
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.92
SVM decision value 2.87
SVM RNA-class probability 0.997495
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5363797 116 - 27905053
-AAACAGC--AUAAAUAUAGUGCAUUGCAUUUUAUACUAAUUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUA-GCAAAAGAAAAAAAAACCAACAAGAAAACCAAACA
-.......--.......(((((((...((.((..(((.....)))..)).))........((((((....)))))).)))))))-................................... ( -17.80)
>DroSec_CAF1 23247 109 - 1
-AACCAGC--AUAAAUAUAGUGCAUUGCAUUUUAUACUAAUUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUA-GCAAAAGAAAAAAAA----A---CAAAACCAAACA
-.......--.......(((((((...((.((..(((.....)))..)).))........((((((....)))))).)))))))-...............----.---............ ( -17.80)
>DroSim_CAF1 22680 113 - 1
-AACCAGC--AUAAAUAUAGUGCAUUGCAUUUUAUACUAAUUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUA-GCAAAAGAAAAAAAAAACAA---CAAAACCAAACA
-.......--.......(((((((...((.((..(((.....)))..)).))........((((((....)))))).)))))))-....................---............ ( -17.80)
>DroEre_CAF1 23446 108 - 1
-AACCAGC--AUAAAUAUAGUGCAUUGCAUUUUAUACUAAUUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUA-GCAAAAAACAAAACA----A----AAAAACAAACA
-.......--.......(((((((...((.((..(((.....)))..)).))........((((((....)))))).)))))))-...............----.----........... ( -17.80)
>DroAna_CAF1 23184 112 - 1
GAACAAACAAAUAAUUAUACUGCAUUGCAUUUUAUACUAAUUAUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUAAGCAAAAACCAAAA----CAA---CAAGG-AUAAAA
..........(((((((...(((...)))........)))))))...........((...((((((....))))))((((.....)))).........----...---...))-...... ( -10.60)
>consensus
_AACCAGC__AUAAAUAUAGUGCAUUGCAUUUUAUACUAAUUGUACGAACUGAACCCACUGAAGAAGUUCUUCUUCUUGCACUA_GCAAAAGAAAAAAAA__CAA___CAAAACCAAACA
.................(((((((...((.((..(((.....)))..)).))........((((((....)))))).))))))).................................... (-15.06 = -15.46 +   0.40)

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 10:21:32 2006