Locus 7460

Sequence ID 3L_DroMel_CAF1
Location 20,019,307 – 20,019,447
Length 140
Max. P 0.998782
window12122 window12123

overview

Window 2

Location 20,019,307 – 20,019,423
Length 116
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 87.47
Mean single sequence MFE -28.44
Consensus MFE -23.02
Energy contribution -23.18
Covariance contribution 0.16
Combinations/Pair 1.23
Mean z-score -1.65
Structure conservation index 0.81
SVM decision value 0.47
SVM RNA-class probability 0.750866
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20019307 116 + 23771897
A-UGGGGCGCCGCGGAAAAAACUUUCGGCGUCAAAUGGAUUAUUCUAAAU--AGGUUAUGUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUU
.-...(((((((.((......))..)))))))...((((....))))...--..(((((.((.....)).)))))((((((((...(((((((..(....)..))))))).)))))))) ( -30.50)
>DroSec_CAF1 11101 118 + 1
A-UGAGGCGCCGCAGAAAAAACUUUUGGCGUCAAAUAGAUUAUUCUAUUCUAUGGUUAUAUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUU
.-...(((((((.(((......)))))))))).((((((....)))))).....(((((.(((....))))))))((((((((...(((((((..(....)..))))))).)))))))) ( -29.80)
>DroSim_CAF1 5759 116 + 1
A-UGAGGCGCCGCAGAAAAAACUUUCGGCGUCAAAUAGAAUAUUCUAAAU--AGGUUAUGUUUCGGCGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUU
.-...(((((((.(((......))))))))))...((((....))))...--..(((((.((.....)).)))))((((((((...(((((((..(....)..))))))).)))))))) ( -30.50)
>DroEre_CAF1 10637 115 + 1
AGCGAGGCGUUGCAGAAAAAACUUUCGGCGUCAAAUAGAUUAUUCUAAAU--AGGCAAUGUUUCGGGGAAAUGACAAAGCGAAAAGUUCUUU--GGGAACUUUUAAAGGAAUUUGCUGU
..(((((((((((.((((....)))).........((((....))))...--..)))))))))))((.((((..(......((((((((...--..))))))))...)..)))).)).. ( -29.60)
>DroYak_CAF1 12604 115 + 1
AGUGAGACGUUGCAGAAAAAACUUUGGGCGUCAAAUAGAUUAUUCUAAAU--AGGUUAUGUUUCGGGGAAAUGACAAAGCGAAAGGUCCUUU--AGAACUUUGAAAAGGAAUUUUCUUU
.....((((((.((((......))))))))))...((((....))))...--..(((.((((..........)))).)))(((((.((((((--..........)))))).)))))... ( -21.80)
>consensus
A_UGAGGCGCCGCAGAAAAAACUUUCGGCGUCAAAUAGAUUAUUCUAAAU__AGGUUAUGUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUU
.....(((((((.(((......))))))))))...((((....)))).......(((((.(((....))))))))((((((((...((((((((((....)))))))))).)))))))) (-23.02 = -23.18 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,019,346 – 20,019,447
Length 101
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 89.96
Mean single sequence MFE -23.80
Consensus MFE -22.88
Energy contribution -23.04
Covariance contribution 0.16
Combinations/Pair 1.18
Mean z-score -2.06
Structure conservation index 0.96
SVM decision value 3.22
SVM RNA-class probability 0.998782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20019346 101 + 23771897
UAUUCUAAAU--AGGUUAUGUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUUGUACAUUUAUAUUUAAAUGAGGCC
..........--.(((..(((((..(..(((((((((((((((...(((((((..(....)..))))))).)))))))))).)))))...)..)))))..))) ( -26.80)
>DroSec_CAF1 11140 103 + 1
UAUUCUAUUCUAUGGUUAUAUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUUGUACAUUUAUAUUUAAAUGAGGCC
.............(((..(((((..(..(((((((((((((((...(((((((..(....)..))))))).)))))))))).)))))...)..)))))..))) ( -27.60)
>DroSim_CAF1 5798 101 + 1
UAUUCUAAAU--AGGUUAUGUUUCGGCGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUUGUACAUUUAUAUUUAAAUGAGGCC
..........--.(((..(((((..(..(((((((((((((((...(((((((..(....)..))))))).)))))))))).)))))...)..)))))..))) ( -25.70)
>DroEre_CAF1 10677 99 + 1
UAUUCUAAAU--AGGCAAUGUUUCGGGGAAAUGACAAAGCGAAAAGUUCUUU--GGGAACUUUUAAAGGAAUUUGCUGUGUACAUUUAUAUUUAAAUGAGGCC
..........--.(((..(((((..(..((((((((.((((((...((((((--(((....))))))))).)))))).))).)))))...)..)))))..))) ( -22.30)
>DroYak_CAF1 12644 99 + 1
UAUUCUAAAU--AGGUUAUGUUUCGGGGAAAUGACAAAGCGAAAGGUCCUUU--AGAACUUUGAAAAGGAAUUUUCUUUGUACAUUUAUAUUUAAAUGAGGUC
.....(((((--(....((((..((((((((........(....).((((((--..........))))))..)))))))).))))...))))))......... ( -16.60)
>consensus
UAUUCUAAAU__AGGUUAUGUUUCGGGGAGAUGACAAAGCGAAAAGUUCUUUUUGGAACUUUGAAAAGGAAUUUGCUUUGUACAUUUAUAUUUAAAUGAGGCC
.............(((..(((((..(..(((((((((((((((...((((((((((....)))))))))).)))))))))).)))))...)..)))))..))) (-22.88 = -23.04 +   0.16)

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 12:47:40 2006