Locus 1027

Sequence ID 2R_DroMel_CAF1
Location 4,231,338 – 4,231,450
Length 112
Max. P 0.999317
window1824 window1825

overview

Window 4

Location 4,231,338 – 4,231,450
Length 112
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 78.61
Mean single sequence MFE -33.98
Consensus MFE -24.31
Energy contribution -25.27
Covariance contribution 0.96
Combinations/Pair 1.20
Mean z-score -3.24
Structure conservation index 0.72
SVM decision value 3.38
SVM RNA-class probability 0.999118
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4231338 112 + 20766785
-----CCUAUUAAAAGAGUCCUAGAAACCUCGAAGGAUUUAAGAAGGCUAUUUAAGCUUUACUAAAGUAAAGUGGCGAUUUAAAUCUUUUGAGGUCUCUGUAACUCCACCGAUUAUA
-----..........((((..((((.(((((((((((((((((...(((......(((((((....))))))))))..))))))))))))))))).))))..))))........... ( -37.00)
>DroSec_CAF1 833 99 + 1
-----CCUUCUAAGGGAGUCCCAGAAACCUCUAGUGAUUUCAGAAGGCUAUUUUCGC-------------GGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCACCGAUUGUA
-----.........(((((..((((.(((((....(((((.(((..((((((.....-------------))))))..))))))))....))))).))))..))))).......... ( -32.70)
>DroSim_CAF1 832 107 + 1
-----CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUUUACAGA-----AGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCGCCGAUUGUA
-----.........(((((..((((.(((((.(.(((((((((...(((((((..(.....)..)-----))))))..))))))))).).))))).))))..))))).......... ( -39.40)
>DroEre_CAF1 840 111 + 1
AAGAACCUUAUAAGGAAGUCCAAGAAACCGCUAGGGAUUUAAGAAAGCUACUUUCGUUU-GCCGA-----AGUAGCGGUUUAAAUCUGUUGCGGUCUUUGUAACUCCCCCGAUUGUA
.............((.(((...(((.(((((.(.(((((((((...((((((((.(...-.).))-----))))))..))))))))).).))))).)))...))).))......... ( -34.20)
>DroYak_CAF1 840 111 + 1
AUGAACCUUUUAAGGAAUUCCCAGAAACCUCUACGGAUUUAAGAAGGCUAAUUUGGCUG-AAUGA-----AGUAGCGGUUUAAAUCUGUUGAGCUCUCUGAAUUUCCCCCGAUUGUA
.............((((....((((...(((.(((((((((((...((((.((((....-..)))-----).))))..))))))))))).)))...))))...)))).......... ( -26.60)
>consensus
_____CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUU_ACUGA_____AGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCACCGAUUGUA
..............(((((..((((.(((((.(.(((((((((...((((((..................))))))..))))))))).).))))).))))..))))).......... (-24.31 = -25.27 +   0.96) 

alignment

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secondary structure

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dotplot

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Window 5

Location 4,231,338 – 4,231,450
Length 112
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -32.56
Consensus MFE -23.79
Energy contribution -24.51
Covariance contribution 0.72
Combinations/Pair 1.14
Mean z-score -3.37
Structure conservation index 0.73
SVM decision value 3.51
SVM RNA-class probability 0.999317
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4231338 112 - 20766785
UAUAAUCGGUGGAGUUACAGAGACCUCAAAAGAUUUAAAUCGCCACUUUACUUUAGUAAAGCUUAAAUAGCCUUCUUAAAUCCUUCGAGGUUUCUAGGACUCUUUUAAUAGG-----
....((..(.((((((..(((((((((.((.(((((((........(((((....)))))(((.....)))....))))))).)).)))))))))..)))))).)..))...----- ( -30.70)
>DroSec_CAF1 833 99 - 1
UACAAUCGGUGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACC-------------GCGAAAAUAGCCUUCUGAAAUCACUAGAGGUUUCUGGGACUCCCUUAGAAGG-----
.......((.(((((..((((((((((....(((((.....((((..-------------.......))))......)))))....))))))))))..))))))).......----- ( -31.70)
>DroSim_CAF1 832 107 - 1
UACAAUCGGCGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACU-----UCUGUAAAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAGAAGG-----
.......((.(((((..((((((((((....(((((((...((((.(-----(.((.....)).)).))))....)))))))....))))))))))..))))))).......----- ( -35.00)
>DroEre_CAF1 840 111 - 1
UACAAUCGGGGGAGUUACAAAGACCGCAACAGAUUUAAACCGCUACU-----UCGGC-AAACGAAAGUAGCUUUCUUAAAUCCCUAGCGGUUUCUUGGACUUCCUUAUAAGGUUCUU
.......(((((((((.((((((((((....(((((((...((((((-----(((..-...)).)))))))....)))))))....))))))).))))))))))))........... ( -37.40)
>DroYak_CAF1 840 111 - 1
UACAAUCGGGGGAAAUUCAGAGAGCUCAACAGAUUUAAACCGCUACU-----UCAUU-CAGCCAAAUUAGCCUUCUUAAAUCCGUAGAGGUUUCUGGGAAUUCCUUAAAAGGUUCAU
...((((.((((((.((((((((.(((.((.(((((((...((((..-----.....-.........))))....))))))).)).))).))))))))..))))))....))))... ( -27.99)
>consensus
UACAAUCGGGGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACU_____UCAGU_AAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAAAAGG_____
.......((.((((((.((((((((((....(((((((...((((......................))))....)))))))....)))))))))).))))))))............ (-23.79 = -24.51 +   0.72) 

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 09:54:39 2006