Locus 1554

Sequence ID 3R_DroMel_CAF1
Location 4,456,416 – 4,456,508
Length 92
Max. P 0.956248
window2567 window2568

overview

Window 7

Location 4,456,416 – 4,456,508
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.58
Mean single sequence MFE -25.95
Consensus MFE -15.71
Energy contribution -16.13
Covariance contribution 0.42
Combinations/Pair 1.30
Mean z-score -2.12
Structure conservation index 0.61
SVM decision value 0.83
SVM RNA-class probability 0.861906
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4456416 92 + 27905053
UAUGCCCGGCCACUUGACAAAUUAAUGCACGCUAAUGCGGCACAAAUUUUGU-ACUUCAAGAGGCCGUUGAAUUUUGCGAAAUGCGCAGCG------AA
..(((.(((((.(((((((((....(((.(((....)))))).....)))).-...))))).)))))........((((.....)))))))------.. ( -29.70)
>DroSec_CAF1 8400 92 + 1
UAUGCCCGGCCACUUGACAAAUUAAUGCACGCUAAUGCGGCACAAAUUUUGU-ACUUCAAGAGGCUGUUGAAUUUUGCGGAAUGCGCACAG------AA
......(((((.(((((((((....(((.(((....)))))).....)))).-...))))).)))))........((((.....))))...------.. ( -25.50)
>DroSim_CAF1 8813 92 + 1
UAUGCCCGGCCACUUGACAAAUUAAUGCACGCUAAUGCGGCACAAAUUUUGU-ACUUCAAGAGGCUGUUGAAUUUUGCGGAAUGCGCACAG------AA
......(((((.(((((((((....(((.(((....)))))).....)))).-...))))).)))))........((((.....))))...------.. ( -25.50)
>DroYak_CAF1 8573 92 + 1
UAUGCCCGGCCACUUGACAAAUUAAUGCACGCUAAUGCGGCACAAAUUUUGU-ACUUCAAGAGGCCGUUGAAUUUUGCAAAGUGCGCAGGG------AA
....(((((((.(((((((((....(((.(((....)))))).....)))).-...))))).)))).........(((.......))))))------.. ( -29.30)
>DroAna_CAF1 8255 83 + 1
UAUUUCAGAGCACUUGACAAAUUAAUGCAGGCUAAUGCCGCACAAAUUUUCUUGCUCGAAGAGGCCACAGAAAUUUUCAGAAU----------------
...(((.(((((...((.(((((..(((.(((....))))))..))))))).)))))(((((..(....)...))))).))).---------------- ( -19.90)
>DroPer_CAF1 11012 94 + 1
UAUUUCAGGGAACUUGGCGGAUUAAUGCACGCUAAUGCCGCGCAAAUU-UGU-GCUUCAAGAGGCCUUUUAAA---GCAGAAUGCGCUUAGAAGGAAAA
..((((..((...((((((..........))))))..))(((((...(-(.(-((((.((((....)))).))---))).))))))).......)))). ( -25.80)
>consensus
UAUGCCCGGCCACUUGACAAAUUAAUGCACGCUAAUGCGGCACAAAUUUUGU_ACUUCAAGAGGCCGUUGAAUUUUGCAGAAUGCGCACAG______AA
......(((((.(((((((((....(((.(((....)))))).....))))).....)))).)))))................................ (-15.71 = -16.13 +   0.42)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,456,416 – 4,456,508
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 79.58
Mean single sequence MFE -27.12
Consensus MFE -17.59
Energy contribution -19.57
Covariance contribution 1.97
Combinations/Pair 1.19
Mean z-score -2.63
Structure conservation index 0.65
SVM decision value 1.46
SVM RNA-class probability 0.956248
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4456416 92 - 27905053
UU------CGCUGCGCAUUUCGCAAAAUUCAACGGCCUCUUGAAGU-ACAAAAUUUGUGCCGCAUUAGCGUGCAUUAAUUUGUCAAGUGGCCGGGCAUA
..------.((((((.....))).........(((((.(((((...-...(((((.(((((((....))).)))).))))).))))).))))))))... ( -34.20)
>DroSec_CAF1 8400 92 - 1
UU------CUGUGCGCAUUCCGCAAAAUUCAACAGCCUCUUGAAGU-ACAAAAUUUGUGCCGCAUUAGCGUGCAUUAAUUUGUCAAGUGGCCGGGCAUA
..------.(((((((.....)).........(.(((.(((((...-...(((((.(((((((....))).)))).))))).))))).))).).))))) ( -28.10)
>DroSim_CAF1 8813 92 - 1
UU------CUGUGCGCAUUCCGCAAAAUUCAACAGCCUCUUGAAGU-ACAAAAUUUGUGCCGCAUUAGCGUGCAUUAAUUUGUCAAGUGGCCGGGCAUA
..------.(((((((.....)).........(.(((.(((((...-...(((((.(((((((....))).)))).))))).))))).))).).))))) ( -28.10)
>DroYak_CAF1 8573 92 - 1
UU------CCCUGCGCACUUUGCAAAAUUCAACGGCCUCUUGAAGU-ACAAAAUUUGUGCCGCAUUAGCGUGCAUUAAUUUGUCAAGUGGCCGGGCAUA
..------...(((((.....)).........(((((.(((((...-...(((((.(((((((....))).)))).))))).))))).))))).))).. ( -32.70)
>DroAna_CAF1 8255 83 - 1
----------------AUUCUGAAAAUUUCUGUGGCCUCUUCGAGCAAGAAAAUUUGUGCGGCAUUAGCCUGCAUUAAUUUGUCAAGUGCUCUGAAAUA
----------------.......................((((((((.(((((((.(((((((....))).)))).))))).))...))))).)))... ( -19.70)
>DroPer_CAF1 11012 94 - 1
UUUUCCUUCUAAGCGCAUUCUGC---UUUAAAAGGCCUCUUGAAGC-ACA-AAUUUGCGCGGCAUUAGCGUGCAUUAAUCCGCCAAGUUCCCUGAAAUA
.((((.......(((((...(((---(((((........)))))))-)..-....)))))((((((((......)))))..))).........)))).. ( -19.90)
>consensus
UU______CUCUGCGCAUUCCGCAAAAUUCAACGGCCUCUUGAAGU_ACAAAAUUUGUGCCGCAUUAGCGUGCAUUAAUUUGUCAAGUGGCCGGGCAUA
...........((((.....))))........(((((.(((((.......(((((.(((((((....))).)))).))))).))))).)))))...... (-17.59 = -19.57 +   1.97)

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 10:13:24 2006