Locus 109

Sequence ID 4_DroMel_CAF1
Location 772,721 – 773,001
Length 280
Max. P 0.824381
window166 window167 window168

overview

Window 6

Location 772,721 – 772,841
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -30.19
Consensus MFE -15.99
Energy contribution -16.30
Covariance contribution 0.31
Combinations/Pair 1.55
Mean z-score -2.07
Structure conservation index 0.53
SVM decision value 0.69
SVM RNA-class probability 0.824381
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 772721 120 - 1281640
UUUUCAACCUGAUAUGCUGAAAUAGGUUUUCCUCCAUCAUCUUCUGGUUUUUUCCAUUUGAGCUUACAGCUGUCUUUAGUAACAUCUUUAACAUCCAAGGGACCCCUUGGUUUGCUUGGA
.....((((.((...(.(((...(((....)))...))).).)).)))).......((..(((..((.((((....))))...............(((((....)))))))..)))..)) ( -25.00)
>DroVir_CAF1 1655 120 - 1
UUUUCGACUUGGUAAGCCGUGAUGGGUUUACCACCAUCAUCAUCUGGCUUUUGCCACUUCAAUUUACAACUAUCUUUGGUAAUAUCUUUUACAGCUAAAGGACCCUUUGGUUUACCGGGA
.......((((((((((((((((((........)))))))....((((....))))................((((((((..((.....))..)))))))).......))))))))))). ( -36.70)
>DroPse_CAF1 1284 120 - 1
UUUUCCACUUGGUAAGCCGUGAUGGGCUUGCCACCAUCAUCCUCAGGUUUCUUCCAUUUGAGCUUGCAACUGUCUUUAGUAACGUCCUUCACAUCCAAUGGUCCCUUUGGCUUACCCGGC
.......((.((((((((((((.((((..........((..(((((((.......)))))))..))..((((....))))...)))).)))).......(....)...)))))))).)). ( -32.20)
>DroWil_CAF1 1770 120 - 1
UUCUCGACUUGGUAGGCGGUAAUUGGCUUGCCCCCGUCAUCUUCAGGCUUCUGCCAUUUCAGUUUGCAGCUAUCCUUGGUGACAUCUUUCACAGUCAAAGGACCCUUUGGUUUGCCCGGU
......(((.((((((((((((.....)))))...((((((...(((...((((...........))))....))).))))))............(((((....)))))))))))).))) ( -31.80)
>DroMoj_CAF1 2254 120 - 1
UUUUCUACUUGGUAGGCUGUAAUUGGCUUACCACCGUCAUCUUCUGGCUUUUGCCAUUUUAAUUUGCAACUAUCUUUCGUAAUAUCUUUGACAUCUAGGGGACCCUUUGGUUUACCCGGA
.........(((((((((......)))))))))((((((.....((((....)))).......((((...........))))......)))).....(((((((....))))..))))). ( -31.50)
>DroAna_CAF1 3668 120 - 1
UUUUCCACCUGAUAGGCUGUUAUAGGAACUCCACCAUCAUCAUUAGGCUUUUUCCAUUUCAGUUUACAGCUAUCUUUUGUAAUAUCUGUCACAGCUAAGGGCCCCAUUGGUUUUCCAGGA
.......((((..(((((......((....)).............(((((((.......(((.((((((.......))))))...)))........))))))).....)))))..)))). ( -23.96)
>consensus
UUUUCCACUUGGUAGGCUGUAAUAGGCUUACCACCAUCAUCUUCAGGCUUUUGCCAUUUCAGUUUACAACUAUCUUUAGUAACAUCUUUCACAGCCAAGGGACCCUUUGGUUUACCCGGA
..........((((((((......)))))))).((..........((......)).............((((....))))..............((((((....)))))).......)). (-15.99 = -16.30 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 772,841 – 772,961
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.44
Mean single sequence MFE -40.05
Consensus MFE -30.41
Energy contribution -31.75
Covariance contribution 1.34
Combinations/Pair 1.23
Mean z-score -2.39
Structure conservation index 0.76
SVM decision value -0.04
SVM RNA-class probability 0.512435
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 772841 120 + 1281640
GUUUGAUAAAAAACAAGGUCGUUGGGUCCCUCUUGGUCGAACGUCUGCCAAUGAUACCGAAUUUGAUGUAAAGGGCCUCCAGGAAGGCCAUGAGUAUCAGUUUCGCGUCAAGGCAAUUAA
((((......))))..((.((((.(..(......)..).)))).))(((..((((..((((.((((((.....(((((......))))).....)))))).)))).)))).)))...... ( -35.10)
>DroVir_CAF1 1775 120 + 1
AUUCGAUAAGAAACAAGGUCGAUGGGUACCUGUCGGUCGAGCCUCCGGAAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAAUAUCAGUUUAGGGUUAAAGCCAUCAA
....(((.........(..((((((....))))))..).(((((.(((........)))...(((((((((..((((((....)))))).)).)))))))....)))))......))).. ( -35.50)
>DroGri_CAF1 2562 120 + 1
AUUCGAUAAGAAACAGGGUCGUUGGGUGCCGGUCGGUCGUACCUCCGGCAAUGAUACCGAACUUGAUGUCAAGGGCCUGCAGGAAGGCCAUGAGUAUCAGUUUCGGGUCAAGGCCAUCAA
.(((.....)))....((((......((((((..((.....)).)))))).((((.(((((.(((((((((..(((((......))))).))).)))))).))))))))).))))..... ( -46.20)
>DroWil_CAF1 1890 120 + 1
GUUCGACAAGAAACAAGGUAGAUGGGUACCUGUCGGUCGAACUGCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAAUAUCAGUUUCGGGUCAAGGCCAUCAA
(((((((..((....(((((......))))).)).)))))))((.((((..((((.(((((.(((((((((..((((((....)))))).)).))))))).)))))))))..)))).)). ( -51.20)
>DroMoj_CAF1 2374 120 + 1
GUUUGAUAAGAAACAAGGUCGUUGGGUACCGGUCGGUCGUACCUCUGGCAAUGAUACUGAAUUUGAUGUCAAGGGCCUUCAGGAAGGUCAUGAGUAUCAGUUUCGGGUUAAAGCCAUCAA
..(((((..(((((...((((..((((((.((....)))))))).))))..(((((((.(.((((....))))((((((....)))))).).)))))))))))).(((....)))))))) ( -36.10)
>DroAna_CAF1 3788 120 + 1
GUUUGAUAAAAAACAAGGACGAUGGGUACCUGUUGGUCGAUCUUCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGUCUUCAGGAAGGCCAUGAGUAUCAGUUUCGAGUCAGAGCCAUUAA
((((......))))..(..((((((....))))))..).......((((..((((..((((.(((((((((..((((((....)))))).))).)))))).)))).))))..)))).... ( -36.20)
>consensus
GUUCGAUAAGAAACAAGGUCGAUGGGUACCUGUCGGUCGAACCUCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAGUAUCAGUUUCGGGUCAAAGCCAUCAA
(((((((..((....((((........)))).)).)))))))....(((..((((.(((((.(((((((((..((((((....)))))).))).)))))).)))))))))..)))..... (-30.41 = -31.75 +   1.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 772,881 – 773,001
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.28
Mean single sequence MFE -40.80
Consensus MFE -30.91
Energy contribution -30.50
Covariance contribution -0.41
Combinations/Pair 1.33
Mean z-score -2.28
Structure conservation index 0.76
SVM decision value 0.05
SVM RNA-class probability 0.559189
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 772881 120 + 1281640
ACGUCUGCCAAUGAUACCGAAUUUGAUGUAAAGGGCCUCCAGGAAGGCCAUGAGUAUCAGUUUCGCGUCAAGGCAAUUAAUGAAGAGGGGGAAUCCGAUCCCCUGGACUCCGAUGAUAGC
.((((((((..((((..((((.((((((.....(((((......))))).....)))))).)))).)))).))))...........((((((......)))))).......))))..... ( -38.40)
>DroVir_CAF1 1815 120 + 1
GCCUCCGGAAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAAUAUCAGUUUAGGGUUAAAGCCAUCAAUGAGGAAGGUGAAUCCGAGCCUCUAGAGACCGAUGGAAGU
.((..(((...((((.(..((((.(((((((..((((((....)))))).)).)))))))))..)(((....)))))))..((((..((.....))...))))......)))..)).... ( -36.40)
>DroGri_CAF1 2602 120 + 1
ACCUCCGGCAAUGAUACCGAACUUGAUGUCAAGGGCCUGCAGGAAGGCCAUGAGUAUCAGUUUCGGGUCAAGGCCAUCAACGAGGAGGGCGAAUCCGAACCUCUGGAGACCGAUGGCAGC
..(((((((..((((.(((((.(((((((((..(((((......))))).))).)))))).)))))))))..)))......((((.(((....)))...)))).))))............ ( -46.90)
>DroWil_CAF1 1930 120 + 1
ACUGCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAAUAUCAGUUUCGGGUCAAGGCCAUCAAUGAAGAGGGUGAAUCGGAACCUCUCGAGACCGAUGGCAGC
.((((((((..((((.(((((.(((((((((..((((((....)))))).)).))))))).)))))))))..)))(((......((((((........))).)))......)))))))). ( -47.90)
>DroMoj_CAF1 2414 120 + 1
ACCUCUGGCAAUGAUACUGAAUUUGAUGUCAAGGGCCUUCAGGAAGGUCAUGAGUAUCAGUUUCGGGUUAAAGCCAUCAAUGAGGAAGGUGAAUCUGAACCUUUGGAGACCGAUGGUAGC
((((..(((..(((((((.(.((((....))))((((((....)))))).).))))))))))..))))....((((((......((((((........))))))(....).))))))... ( -37.00)
>DroAna_CAF1 3828 120 + 1
UCUUCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGUCUUCAGGAAGGCCAUGAGUAUCAGUUUCGAGUCAGAGCCAUUAAUGAAGAGGGUGAAUCUGAACCUCUUGAAACAGAUGGCAGC
...((((((........((((.(((((((((..((((((....)))))).))).)))))).)))).))))))((((((..(.((((((...........)))))).)....))))))... ( -38.20)
>consensus
ACCUCUGGCAAUGAUACCGAAUUUGAUGUCAAGGGCCUUCAGGAAGGCCAUGAGUAUCAGUUUCGGGUCAAAGCCAUCAAUGAAGAGGGUGAAUCCGAACCUCUGGAGACCGAUGGCAGC
...........((((.(((((.(((((((((..((((((....)))))).))).)))))).)))))))))..((((((.....((.((((........)))))).......))))))... (-30.91 = -30.50 +  -0.41)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:48 2006