Locus 1418

Sequence ID 3R_DroMel_CAF1
Location 4,100,684 – 4,100,918
Length 234
Max. P 0.998064
window2358 window2359 window2360 window2361 window2362

overview

Window 8

Location 4,100,684 – 4,100,804
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.17
Mean single sequence MFE -39.07
Consensus MFE -36.61
Energy contribution -36.45
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.26
Structure conservation index 0.94
SVM decision value 0.63
SVM RNA-class probability 0.805056
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4100684 120 - 27905053
GCCGACUUUGAUGCGGCAAUUCGAGCGCGGUGGUGUUGUUUUGCCAACAUUACUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGUGAUCCUUUUAUCCUUCAU
((((.(......))))).....((((((((((((((((......)))))))))))).(((((.(......).)))))...)).((((.(((....)))))))..............)).. ( -39.00)
>DroSec_CAF1 12542 120 - 1
GCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAAUGCUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGUGAUCCUUUUAUCCUUCAU
((((.(......))))).......(.((((..((((((((.....))))))))..)))).)......(((((.(((.......((((.(((....))))))).........)))))))). ( -38.09)
>DroSim_CAF1 12605 120 - 1
GCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGUGAUCCUUUUAUCCUUCAU
...((..(((((.(((((...((....))(..((((((......))))))..)))))))))))..))(((((.(((.......((((.(((....))))))).........)))))))). ( -37.59)
>DroEre_CAF1 12681 120 - 1
GCCGACUUUGAUGCGGCAAUUCGAACUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGUGAUCCCUUUAUCCCUCAU
...((..(((((.(((((...((....))(..((((((......))))))..)))))))))))..))(((((.(((.......((((.(((....))))))).........)))))))). ( -40.29)
>DroYak_CAF1 12675 120 - 1
GCAGGCUUUGAUGCGGCAAUUCGAACUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGAGAUCCCCUUAUCCCUCAU
.((((..(((((.(((((...((....))(..((((((......))))))..)))))))))))..))))(((.(((((......(((.(((....))))))))))).))).......... ( -40.40)
>consensus
GCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUCGCAACUGACUGGCGCCAGCAGUGAUCCUUUUAUCCUUCAU
...((..(((((.(((((...((....))(((((((((......)))))))))))))))))))..))(((((.(((.......((((.(((....))))))).........)))))))). (-36.61 = -36.45 +  -0.16)

alignment

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secondary structure

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Window 9

Location 4,100,724 – 4,100,844
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.08
Mean single sequence MFE -35.32
Consensus MFE -29.00
Energy contribution -30.40
Covariance contribution 1.40
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.82
SVM decision value 1.74
SVM RNA-class probability 0.974873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4100724 120 + 27905053
GAAGAUCACCUCAGAUACUGAUCGGCAGUAAUGUUGGCAAAACAACACCACCGCGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGGUCCGAUCCAAUCUGGGCA
.........(((((((...((((((.......((((......))))((((..((((.......).)))......((((((((......)))))..))).))))))))))..))))))).. ( -35.30)
>DroSec_CAF1 12582 120 + 1
GAAGAUCACCUCAGAUACUGAUCGGCAGCAUUGUUGGCAAAACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCA
..........(((((...((((((((((...(((((......)))))....((....))..)))))).))))......((((......)))))))))..(((((((((...))))))))) ( -37.60)
>DroSim_CAF1 12645 120 + 1
GAAGAUCACCUCAGAUACUGAUCGGCAGCAAUGUUGGCAAAACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCA
..........(((((...((((((((((...(((((......)))))....((....))..)))))).))))......((((......)))))))))..(((((((((...))))))))) ( -37.70)
>DroEre_CAF1 12721 120 + 1
GAAGAUCACCUCAGAUACUGAUCGGCAGCAAUGUUGGCAAAACAACACCACCGAGUUCGAAUUGCCGCAUCAAAGUCGGCGACAAAUAUCGCUCUGACAUGCCCCGAUCCAAUCUGGGCA
.........(((((((...((((((..(((((((.(((((..((((........))).)..)))))))))....((((((((......)))))..))).))).))))))..))))))).. ( -36.20)
>DroYak_CAF1 12715 120 + 1
GAAGAUCACCUCAGAUACUGAUCGGCAGCAAUGUUGGCAAAACAACACCACCGAGUUCGAAUUGCCGCAUCAAAGCCUGCGACAAUAAUCGCUCUGACAUGCACCGAUCCAAUCUAGUCA
............((((...((((((..(((.(((((......))))).....((((....((((.((((........)))).))))....)))).....))).))))))..))))..... ( -29.80)
>consensus
GAAGAUCACCUCAGAUACUGAUCGGCAGCAAUGUUGGCAAAACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCUGGGCA
.........(((((((...((((((.((((.(((((......))))).....((((.....(((((((......).))))))........)))).....))))))))))..))))))).. (-29.00 = -30.40 +   1.40)

alignment

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secondary structure

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Window 0

Location 4,100,724 – 4,100,844
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.08
Mean single sequence MFE -44.40
Consensus MFE -39.00
Energy contribution -39.48
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -2.32
Structure conservation index 0.88
SVM decision value 3.00
SVM RNA-class probability 0.998064
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4100724 120 - 27905053
UGCCCAGAUUGGAUCGGACCAUGUCAGAGCGAUUUUUGUCGCCGACUUUGAUGCGGCAAUUCGAGCGCGGUGGUGUUGUUUUGCCAACAUUACUGCCGAUCAGUAUCUGAGGUGAUCUUC
.((((((((..((((((((...))).(..(((...(((((((..........))))))).)))..)((((((((((((......)))))))))))))))))...))))).)))....... ( -46.10)
>DroSec_CAF1 12582 120 - 1
UGCCCCGAUUGGAUCGGAGCAUGUCAGAGCGAUUUUUGUCGCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAAUGCUGCCGAUCAGUAUCUGAGGUGAUCUUC
.((.(((((...))))).))((.(((((.(((...(((((((..........))))))).))).(.((((..((((((((.....))))))))..)))).)....))))).))....... ( -43.10)
>DroSim_CAF1 12645 120 - 1
UGCCCCGAUUGGAUCGGAGCAUGUCAGAGCGAUUUUUGUCGCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUC
.((.(((((...))))).))((.((((((((((....))))).....(((((.(((((...((....))(..((((((......))))))..)))))))))))..))))).))....... ( -42.70)
>DroEre_CAF1 12721 120 - 1
UGCCCAGAUUGGAUCGGGGCAUGUCAGAGCGAUAUUUGUCGCCGACUUUGAUGCGGCAAUUCGAACUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUC
.((((((((..((((((((((((((((((((((((....((((((.(((((.........))))).)))))))))))))))))...))).)))).))))))...))))).)))....... ( -47.50)
>DroYak_CAF1 12715 120 - 1
UGACUAGAUUGGAUCGGUGCAUGUCAGAGCGAUUAUUGUCGCAGGCUUUGAUGCGGCAAUUCGAACUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUC
....(((((..(((((((........((((((..(((((((((........))))))))))))..)))((..((((((......))))))..)))))))))...)))))........... ( -42.60)
>consensus
UGCCCAGAUUGGAUCGGAGCAUGUCAGAGCGAUUUUUGUCGCCGACUUUGAUGCGGCAAUUCGAGCUCGGUGGUGUUGUUUUGCCAACAUUGCUGCCGAUCAGUAUCUGAGGUGAUCUUC
.((((((((..((((((.........(..(((...(((((((..........))))))).)))..).(((((((((((......)))))))))))))))))...))))).)))....... (-39.00 = -39.48 +   0.48)

alignment

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secondary structure

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Window 1

Location 4,100,764 – 4,100,878
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.53
Mean single sequence MFE -35.42
Consensus MFE -27.90
Energy contribution -28.54
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -1.66
Structure conservation index 0.79
SVM decision value 0.40
SVM RNA-class probability 0.721895
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4100764 114 + 27905053
AACAACACCACCGCGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGGUCCGAUCCAAUCUGGGCAGAUA------CGCUCAUAAGGAGCACGGAGCUGAUGUGCC
............(((((((..(((((((......).))))))........((((((.....(((((........))))).....------.((((.....)))).))))))))).)))). ( -35.00)
>DroSec_CAF1 12622 114 + 1
AACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCAGAUA------CGCUCAUAAGGAGCACGGAGUGGAUGUGCC
..............((.((..(((((((......).))))))......((((((((...(((((((((...)))))))))....------.((((.....)))).)))))))).)).)). ( -39.30)
>DroSim_CAF1 12685 114 + 1
AACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCAGAUA------CGCUCAUAAGGAGCACGGAGUGGAUGUGCC
..............((.((..(((((((......).))))))......((((((((...(((((((((...)))))))))....------.((((.....)))).)))))))).)).)). ( -39.30)
>DroEre_CAF1 12761 114 + 1
AACAACACCACCGAGUUCGAAUUGCCGCAUCAAAGUCGGCGACAAAUAUCGCUCUGACAUGCCCCGAUCCAAUCUGGGCAGAUA------CGCUCAUAAGGAGCACGGAGCUGAUGUGCC
...........((....))..(((((((......).))))))...(((((((((((...(((((.(((...))).)))))....------.((((.....)))).)))))).)))))... ( -36.80)
>DroYak_CAF1 12755 120 + 1
AACAACACCACCGAGUUCGAAUUGCCGCAUCAAAGCCUGCGACAAUAAUCGCUCUGACAUGCACCGAUCCAAUCUAGUCAGAUACUUGUCCGCUCAUAAGGAGCACGGAGCUGAUGUGCC
.....(((....((((....((((.((((........)))).))))....))))...((.((.(((.....((((....))))........((((.....)))).))).))))..))).. ( -26.70)
>consensus
AACAACACCACCGAGCUCGAAUUGCCGCAUCAAAGUCGGCGACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCUGGGCAGAUA______CGCUCAUAAGGAGCACGGAGCUGAUGUGCC
.....(((.............(((((((......).)))))).....(((((((((...(((((.(((...))).)))))...........((((.....)))).)))))).)))))).. (-27.90 = -28.54 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,100,804 – 4,100,918
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.73
Mean single sequence MFE -35.97
Consensus MFE -29.76
Energy contribution -30.20
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.83
SVM decision value 1.09
SVM RNA-class probability 0.913393
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4100804 114 + 27905053
GACAAAAAUCGCUCUGACAUGGUCCGAUCCAAUCUGGGCAGAUA------CGCUCAUAAGGAGCACGGAGCUGAUGUGCCAUCCCUCAGCCGGAUGAUAACCAUCAGUAGGCAAUCUAUG
(.((...(((((((((.....(((((........))))).....------.((((.....)))).)))))).))).)).)........(((.((((.....))))....)))........ ( -32.00)
>DroSec_CAF1 12662 114 + 1
GACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCAGAUA------CGCUCAUAAGGAGCACGGAGUGGAUGUGCCAUCCCUCAGCCGGAUGAUAACCAUCAGUAGGCAAUCUAUG
..........((((((...(((((((((...)))))))))....------.((((.....)))).))))))(((((...)))))....(((.((((.....))))....)))........ ( -39.40)
>DroSim_CAF1 12725 114 + 1
GACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCGGGGCAGAUA------CGCUCAUAAGGAGCACGGAGUGGAUGUGCCAUCCCUCAGCCGGAUGAUAACCAUCAGUAGGCAAUCUAUG
..........((((((...(((((((((...)))))))))....------.((((.....)))).))))))(((((...)))))....(((.((((.....))))....)))........ ( -39.40)
>DroEre_CAF1 12801 114 + 1
GACAAAUAUCGCUCUGACAUGCCCCGAUCCAAUCUGGGCAGAUA------CGCUCAUAAGGAGCACGGAGCUGAUGUGCCAUCCCUCAGCCGGAUGAUAACCAUCAGUAGGCAAUCUAUG
.....(((((((((((...(((((.(((...))).)))))....------.((((.....)))).)))))).)))))...........(((.((((.....))))....)))........ ( -37.70)
>DroYak_CAF1 12795 120 + 1
GACAAUAAUCGCUCUGACAUGCACCGAUCCAAUCUAGUCAGAUACUUGUCCGCUCAUAAGGAGCACGGAGCUGAUGUGCCAUCCCUCAGCCGGAUGAUAAACAUCAGUAGGCAAUCUAUG
............((((((..................))))))...(((((.((((.....)))).....((((((((..(((((.......)))))....)))))))).)))))...... ( -31.37)
>consensus
GACAAAAAUCGCUCUGACAUGCUCCGAUCCAAUCUGGGCAGAUA______CGCUCAUAAGGAGCACGGAGCUGAUGUGCCAUCCCUCAGCCGGAUGAUAACCAUCAGUAGGCAAUCUAUG
(.((...(((((((((...(((((.(((...))).)))))...........((((.....)))).)))))).))).)).)........(((.((((.....))))....)))........ (-29.76 = -30.20 +   0.44)

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 10:10:02 2006