Locus 4506

Sequence ID 2R_DroMel_CAF1
Location 14,805,087 – 14,805,212
Length 125
Max. P 0.996498
window7212 window7213 window7214 window7215

overview

Window 2

Location 14,805,087 – 14,805,184
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 89.35
Mean single sequence MFE -28.95
Consensus MFE -22.50
Energy contribution -23.00
Covariance contribution 0.50
Combinations/Pair 1.16
Mean z-score -2.38
Structure conservation index 0.78
SVM decision value 1.15
SVM RNA-class probability 0.922036
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14805087 97 + 20766785
GGUGAGUAUCCAAUGAUUGGGUUAGAAUCCGCAAGAAAUGCCGUAAACUACCGGCCUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGG
..(((((......(((.((((((((((..(....)....((((........))))..)))))))))).)))(((((((.....))))))).))))). ( -30.30)
>DroSec_CAF1 6983 97 + 1
GGUGAGUAUCCAAAGAUUGCGUUAGAAUCCGCAAGAAAUGCCGUGAAGUACCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCUG
(((..............((((........))))((((((((((........)))))))))).)))......(((((((.....)))))))....... ( -29.10)
>DroSim_CAF1 1068 97 + 1
GGUGAGUAUCCAAUGAUUGGGUUAGAAUCCGCAAGAAAUGCCGUGAUCUGCCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGG
..(((((......(((.(((((((((...(....).(((((((........)))))))))))))))).)))(((((((.....))))))).))))). ( -32.80)
>DroYak_CAF1 1067 97 + 1
GGUGAGUACUUAAUGAUUGCAUUAAAACCCGCAGGAAAUGCAGUAGACUACCGGCAUUUCUAACCUAUGAAGUGCAUUUUCGCGAUGCACAAUUCGG
.(((.((..((((((....)))))).)).))).((((((((.(((...)))..))))))))......(((((((((((.....)))))))..)))). ( -23.60)
>consensus
GGUGAGUAUCCAAUGAUUGCGUUAGAAUCCGCAAGAAAUGCCGUAAACUACCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGG
(((....(((((.....)))))....)))....((((((((((........))))))))))..........(((((((.....)))))))....... (-22.50 = -23.00 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,805,087 – 14,805,184
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 89.35
Mean single sequence MFE -29.07
Consensus MFE -25.12
Energy contribution -25.75
Covariance contribution 0.62
Combinations/Pair 1.08
Mean z-score -2.79
Structure conservation index 0.86
SVM decision value 2.21
SVM RNA-class probability 0.990440
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14805087 97 - 20766785
CCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAGGCCGGUAGUUUACGGCAUUUCUUGCGGAUUCUAACCCAAUCAUUGGAUACUCACC
((((...(((((((.....)))))))......((((((((..((((........))))...((.....))))))))))......))))......... ( -28.50)
>DroSec_CAF1 6983 97 - 1
CAGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGUACUUCACGGCAUUUCUUGCGGAUUCUAACGCAAUCUUUGGAUACUCACC
.(((((((((((((.....))))))).......((.((((((((((........)))))))))).)).))))))......(((....)))....... ( -31.20)
>DroSim_CAF1 1068 97 - 1
CCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGCAGAUCACGGCAUUUCUUGCGGAUUCUAACCCAAUCAUUGGAUACUCACC
..((((((((((((.....))))))).......((.((((((((((........)))))))))).)).)))))....(((.....)))......... ( -31.40)
>DroYak_CAF1 1067 97 - 1
CCGAAUUGUGCAUCGCGAAAAUGCACUUCAUAGGUUAGAAAUGCCGGUAGUCUACUGCAUUUCCUGCGGGUUUUAAUGCAAUCAUUAAGUACUCACC
..(((..((((((.......)))))))))....((..(((((((.((((...)))))))))))..))(((((((((((....))))))).))))... ( -25.20)
>consensus
CCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGUAGUUCACGGCAUUUCUUGCGGAUUCUAACCCAAUCAUUGGAUACUCACC
..((((((((((((.....))))))).......((.((((((((((........)))))))))).)).)))))........................ (-25.12 = -25.75 +   0.62)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,805,113 – 14,805,212
Length 99
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -29.20
Consensus MFE -27.35
Energy contribution -27.97
Covariance contribution 0.62
Combinations/Pair 1.08
Mean z-score -2.77
Structure conservation index 0.94
SVM decision value 2.71
SVM RNA-class probability 0.996498
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14805113 99 + 20766785
AUCCGCAAGAAAUGCCGUAAACUACCGGCCUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGGA--AAUACCUGCGACAAUAUGGUCGUCCCG
.((((..(((((.((((........)))).)))))..........(((((((.....)))))))....))))--.......(((((......))))).... ( -28.30)
>DroSec_CAF1 7009 101 + 1
AUCCGCAAGAAAUGCCGUGAAGUACCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCUGAAAAAUACCUGCGACAAUAUGGUCGUCCCG
....(((((((((((((........))))))))))..........(((((((.....)))))))................)))(((......)))...... ( -28.60)
>DroSim_CAF1 1094 101 + 1
AUCCGCAAGAAAUGCCGUGAUCUGCCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGGAAAAAUACCUGCGACAAUAUGGUCGUCCCG
.((((..((((((((((........))))))))))..........(((((((.....)))))))....)))).........(((((......))))).... ( -32.60)
>DroYak_CAF1 1093 101 + 1
ACCCGCAGGAAAUGCAGUAGACUACCGGCAUUUCUAACCUAUGAAGUGCAUUUUCGCGAUGCACAAUUCGGAAAAUUACCUGCGACAUUAUGGUCGUCUCG
....(((((..................(((((((........)))))))((((((.(((........)))))))))..)))))(((......)))...... ( -27.30)
>consensus
AUCCGCAAGAAAUGCCGUAAACUACCGGCAUUUCUAACCUAUUUAGUGCAUUUUCGCAAUGCACAAUUCGGAAAAAUACCUGCGACAAUAUGGUCGUCCCG
.((((..((((((((((........))))))))))..........(((((((.....)))))))....)))).........(((((......))))).... (-27.35 = -27.97 +   0.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,805,113 – 14,805,212
Length 99
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -31.52
Consensus MFE -28.49
Energy contribution -29.80
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.90
SVM decision value 1.55
SVM RNA-class probability 0.963259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14805113 99 - 20766785
CGGGACGACCAUAUUGUCGCAGGUAUU--UCCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAGGCCGGUAGUUUACGGCAUUUCUUGCGGAU
.(.(((((.....))))).).......--(((.....(((((((.....))))))).......((.(((((.((((........)))).))))).))))). ( -31.30)
>DroSec_CAF1 7009 101 - 1
CGGGACGACCAUAUUGUCGCAGGUAUUUUUCAGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGUACUUCACGGCAUUUCUUGCGGAU
.(.(((((.....))))).)........(((......(((((((.....))))))).......((.((((((((((........)))))))))).))))). ( -32.70)
>DroSim_CAF1 1094 101 - 1
CGGGACGACCAUAUUGUCGCAGGUAUUUUUCCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGCAGAUCACGGCAUUUCUUGCGGAU
.(.(((((.....))))).).........(((.....(((((((.....))))))).......((.((((((((((........)))))))))).))))). ( -35.60)
>DroYak_CAF1 1093 101 - 1
CGAGACGACCAUAAUGUCGCAGGUAAUUUUCCGAAUUGUGCAUCGCGAAAAUGCACUUCAUAGGUUAGAAAUGCCGGUAGUCUACUGCAUUUCCUGCGGGU
..(((((((......)))((.((((.((((((.....((((((.......))))))......))..)))).)))).)).)))).(((((.....))))).. ( -26.50)
>consensus
CGGGACGACCAUAUUGUCGCAGGUAUUUUUCCGAAUUGUGCAUUGCGAAAAUGCACUAAAUAGGUUAGAAAUGCCGGUAGUUCACGGCAUUUCUUGCGGAU
.(.(((((.....))))).).........(((.....(((((((.....))))))).......((.((((((((((........)))))))))).))))). (-28.49 = -29.80 +   1.31)

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 11:21:34 2006