Locus 5313

Sequence ID 2L_DroMel_CAF1
Location 15,026,657 – 15,026,802
Length 145
Max. P 0.975813
window8442 window8443 window8444

overview

Window 2

Location 15,026,657 – 15,026,762
Length 105
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.17
Mean single sequence MFE -26.79
Consensus MFE -18.39
Energy contribution -18.95
Covariance contribution 0.56
Combinations/Pair 1.22
Mean z-score -2.02
Structure conservation index 0.69
SVM decision value 1.33
SVM RNA-class probability 0.942840
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15026657 105 + 22407834
UG----AU--CUCUAUUC-GCACAGGUCAUUGAGGUUAUACGUCAUCCCAAGGAUAAGGCCGAAUCGAAAUACAAUCCCGAUUCAGCCAUAUCGAAAGAGGACGAAGAACGC
((----((--(((...((-.....)).....)))))))..((((((((...))))..(((.((((((...........)))))).)))...((....)).))))........ ( -27.10)
>DroGri_CAF1 18883 108 + 1
UA----AUAUAUCAAUUGAUCUUAGGUCAUUGAGGUCAUACGACAUCCAAAGGAUAAGGCCGAAUCAAAGUACAAUCCGGACUCGGCCAUAUCGAAGGAGGAUGAGGAACGC
..----.....((...(((((((((....)))))))))...))(((((.........((((((.((...(......)..)).))))))...((....)))))))........ ( -30.00)
>DroWil_CAF1 34216 106 + 1
UAAAAACU--AUUUUUU--U--AAGGUCAUUGAGGUCAUAAGACAUCCUAAAGAUAAAGCUGAAUCGAAAUAUAAUCCCGAUUCGGCUAUAUCGAAAGAGGAUGAAGAACGU
........--....(((--(--(.(..(.....)..).)))))((((((...((((.((((((((((...........)))))))))).)))).....))))))........ ( -30.20)
>DroMoj_CAF1 22854 105 + 1
GU----AUAUAUUAAU---UUUCAGGUCAUUGAGGUCAUACGACAUCCAAAAGAUAAAGCCGAAUCCAAGUAUAAUCCAGACUCGGCCAUAUCCAAAGAGGAUGAGGAACGC
..----..........---((((.(..(.....)..)......(((((....((((..(((((.((.............)).)))))..))))......))))).))))... ( -19.42)
>DroAna_CAF1 19813 99 + 1
AC----CA--AUCUC-------UAGGUAAUUGAGGUCAUACGACAUCCGAAGGAUAAAGCUGAAUCGAAGUAUAAUCCUGAUUCAGCCAUAUCGAAAGAGGAUGAGGAACGC
.(----(.--(((((-------.........))))).......(((((..........(((((((((...........)))))))))....((....))))))).))..... ( -26.20)
>DroPer_CAF1 31407 99 + 1
UG----CC--U----UUC-G--CAGGUCAUUGAGGUCAUACGACAUCCCAAGGAUAAAGCCGAGUCGAAAUACAAUCCCGAUUCGGCCAUAUCGAAGGAGGAUGAAGAACGC
.(----((--(----(..-.--.........)))))....(..((((((...((((..(((((((((...........)))))))))..))))....).)))))..)..... ( -27.80)
>consensus
UA____AU__AUCUAUU__U__CAGGUCAUUGAGGUCAUACGACAUCCAAAGGAUAAAGCCGAAUCGAAAUACAAUCCCGAUUCGGCCAUAUCGAAAGAGGAUGAAGAACGC
...........................................(((((....((((..(((((((((...........)))))))))..))))......)))))........ (-18.39 = -18.95 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,026,657 – 15,026,762
Length 105
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.17
Mean single sequence MFE -30.00
Consensus MFE -24.83
Energy contribution -24.55
Covariance contribution -0.28
Combinations/Pair 1.29
Mean z-score -2.75
Structure conservation index 0.83
SVM decision value 1.76
SVM RNA-class probability 0.975813
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15026657 105 - 22407834
GCGUUCUUCGUCCUCUUUCGAUAUGGCUGAAUCGGGAUUGUAUUUCGAUUCGGCCUUAUCCUUGGGAUGACGUAUAACCUCAAUGACCUGUGC-GAAUAGAG--AU----CA
..(.((((((((((.....((((.((((((((((..((...))..)))))))))).))))...)))))))((((((............)))))-).....))--).----). ( -35.30)
>DroGri_CAF1 18883 108 - 1
GCGUUCCUCAUCCUCCUUCGAUAUGGCCGAGUCCGGAUUGUACUUUGAUUCGGCCUUAUCCUUUGGAUGUCGUAUGACCUCAAUGACCUAAGAUCAAUUGAUAUAU----UA
.(((.(..(((((......((((.(((((((((.((......))..))))))))).))))....)))))..).)))...(((((((.......)).))))).....----.. ( -28.50)
>DroWil_CAF1 34216 106 - 1
ACGUUCUUCAUCCUCUUUCGAUAUAGCCGAAUCGGGAUUAUAUUUCGAUUCAGCUUUAUCUUUAGGAUGUCUUAUGACCUCAAUGACCUU--A--AAAAAAU--AGUUUUUA
.(((....((((((.....((((.(((.((((((..((...))..)))))).))).))))...))))))....)))..............--.--.......--........ ( -25.80)
>DroMoj_CAF1 22854 105 - 1
GCGUUCCUCAUCCUCUUUGGAUAUGGCCGAGUCUGGAUUAUACUUGGAUUCGGCUUUAUCUUUUGGAUGUCGUAUGACCUCAAUGACCUGAAA---AUUAAUAUAU----AC
.(((.(..(((((.....(((((.(((((((((..(.......)..))))))))).)))))...)))))..).))).................---..........----.. ( -30.70)
>DroAna_CAF1 19813 99 - 1
GCGUUCCUCAUCCUCUUUCGAUAUGGCUGAAUCAGGAUUAUACUUCGAUUCAGCUUUAUCCUUCGGAUGUCGUAUGACCUCAAUUACCUA-------GAGAU--UG----GU
.(((.(..(((((......((((.((((((((((((......))).))))))))).))))....)))))..).)))...((((((.....-------..)))--))----). ( -26.50)
>DroPer_CAF1 31407 99 - 1
GCGUUCUUCAUCCUCCUUCGAUAUGGCCGAAUCGGGAUUGUAUUUCGACUCGGCUUUAUCCUUGGGAUGUCGUAUGACCUCAAUGACCUG--C-GAA----A--GG----CA
..((..(((....((((..((((.((((((.(((..((...))..))).)))))).))))...)))).(((((.((....)))))))...--.-)))----.--.)----). ( -33.20)
>consensus
GCGUUCCUCAUCCUCUUUCGAUAUGGCCGAAUCGGGAUUAUACUUCGAUUCGGCUUUAUCCUUGGGAUGUCGUAUGACCUCAAUGACCUG__A__AAUAGAU__AG____CA
.(((....(((((......((((.((((((((((((.......)))))))))))).))))....)))))....))).................................... (-24.83 = -24.55 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,026,682 – 15,026,802
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.94
Mean single sequence MFE -31.99
Consensus MFE -26.72
Energy contribution -25.83
Covariance contribution -0.89
Combinations/Pair 1.29
Mean z-score -2.61
Structure conservation index 0.84
SVM decision value 1.16
SVM RNA-class probability 0.923777
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15026682 120 - 22407834
AUCGUUGCAAUUCCUCGUUUUCGGUAACAAGUUUCUGAUAGCGUUCUUCGUCCUCUUUCGAUAUGGCUGAAUCGGGAUUGUAUUUCGAUUCGGCCUUAUCCUUGGGAUGACGUAUAACCU
.....(((.......((((.((((.((....)).)))).))))....(((((((.....((((.((((((((((..((...))..)))))))))).))))...))))))).)))...... ( -38.20)
>DroVir_CAF1 18821 120 - 1
AUCGUUGUAAUUCCUCAUUUUCGGUUACCAGUUUUUGAUAGCGUUCCUCGUCCUCCUUCGAUAUGGCCGAGUCUGGAUUGUACUUGGAUUCGGCUUUAUCUUUUGGAUGUCGUAUGACCU
......................(((((...(((......)))...(..(((((......((((.(((((((((..(.......)..))))))))).))))....)))))..)..))))). ( -31.10)
>DroGri_CAF1 18911 120 - 1
AUCGUUGUAGUUCCUCGUUUUCGGUUACUAGUUUUUGAUAGCGUUCCUCAUCCUCCUUCGAUAUGGCCGAGUCCGGAUUGUACUUUGAUUCGGCCUUAUCCUUUGGAUGUCGUAUGACCU
...((..((......((((.((((..(....)..)))).))))..(..(((((......((((.(((((((((.((......))..))))))))).))))....)))))..)))..)).. ( -31.70)
>DroWil_CAF1 34242 120 - 1
AUCGUUGUAGUUCCUCAUUCUCGGUAACCAAUUUCUGAUAACGUUCUUCAUCCUCUUUCGAUAUAGCCGAAUCGGGAUUAUAUUUCGAUUCAGCUUUAUCUUUAGGAUGUCUUAUGACCU
..((((((.(((((........)).)))((.....)))))))).....((((((.....((((.(((.((((((..((...))..)))))).))).))))...))))))........... ( -28.50)
>DroMoj_CAF1 22879 120 - 1
AUCGUUGUAGUUCCUCGUUUUCGGUUACUAGUUUUUGAUAGCGUUCCUCAUCCUCUUUGGAUAUGGCCGAGUCUGGAUUAUACUUGGAUUCGGCUUUAUCUUUUGGAUGUCGUAUGACCU
...((..((......((((.((((..(....)..)))).))))..(..(((((.....(((((.(((((((((..(.......)..))))))))).)))))...)))))..)))..)).. ( -35.50)
>DroAna_CAF1 19832 120 - 1
AUCGUUGCAAUUCCUCAUUUUCGGUAACCAAUUUCUGAUAGCGUUCCUCAUCCUCUUUCGAUAUGGCUGAAUCAGGAUUAUACUUCGAUUCAGCUUUAUCCUUCGGAUGUCGUAUGACCU
...(((((...............))))).............(((.(..(((((......((((.((((((((((((......))).))))))))).))))....)))))..).))).... ( -26.96)
>consensus
AUCGUUGUAAUUCCUCAUUUUCGGUAACCAGUUUCUGAUAGCGUUCCUCAUCCUCUUUCGAUAUGGCCGAAUCGGGAUUAUACUUCGAUUCGGCUUUAUCCUUUGGAUGUCGUAUGACCU
...((((((...........((((..........))))..........(((((......((((.((((((((((((.......)))))))))))).))))....)))))...)))))).. (-26.72 = -25.83 +  -0.89)

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 11:41:10 2006