Locus 2226

Sequence ID 2R_DroMel_CAF1
Location 8,211,077 – 8,211,215
Length 138
Max. P 0.795408
window3665 window3666 window3667

overview

Window 5

Location 8,211,077 – 8,211,181
Length 104
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 85.13
Mean single sequence MFE -25.60
Consensus MFE -20.72
Energy contribution -21.30
Covariance contribution 0.58
Combinations/Pair 1.13
Mean z-score -1.55
Structure conservation index 0.81
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8211077 104 - 20766785
UCAC--------CACUGUGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUG--CUGGCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
....--------.........(((.......(((((((..((((..(((..((((..--..)))).)))--.)))).))))))).................((....))..))).. ( -26.90)
>DroSec_CAF1 6538 104 - 1
UAAC--------CACUGAGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUG--CUGUCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
....--------.........(((.......(((((((..(((((....)))))...--..(((....)--))....))))))).................((....))..))).. ( -22.10)
>DroSim_CAF1 6461 104 - 1
UAAC--------CACUGUGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUUUG--CUGGCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
....--------.....(((.((...((...(((((....)))))....((((((..--(..((....)--)..)...))))))............))...))))).......... ( -25.70)
>DroEre_CAF1 6373 102 - 1
UAGC--------CAC--AGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUC--CGGGCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
..((--------...--.)).(((.......(((((((..(((....((..((((..--..)))).)).--..))).))))))).................((....))..))).. ( -25.90)
>DroYak_CAF1 6451 109 - 1
UAGCUAUCUCAGCAC--AGCAUCGCAACACCUUGGCCACUGCCAAUUAGUUGGCCUU--CUGGCUUCUC--CUGG-CUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
..(((.....)))..--....(((.......(((((((..((((...((..((((..--..)))).)).--.)))-)))))))).................((....))..))).. ( -27.70)
>DroAna_CAF1 8688 93 - 1
-----------------------CCAACACCUUGGUCACUGCCAAUUAGCCGGCUUCCUCCGGGUCCUGGCCUGGCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
-----------------------........(((((((..((((....(((((..(((...)))..))))).)))).)))))))...........(((...((....)).)))... ( -25.30)
>consensus
UAAC________CAC__AGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU__CUGGCUUCUG__CUGGCCUGGCCAAAUUUCAAUUAACGUCAAGAGCAAUCAACGAAA
...............................(((((((..((((..(((..((((......)))).)))...)))).)))))))...........(((...((....)).)))... (-20.72 = -21.30 +   0.58)

alignment

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secondary structure

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Window 6

Location 8,211,117 – 8,211,215
Length 98
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.00
Mean single sequence MFE -31.72
Consensus MFE -18.76
Energy contribution -19.18
Covariance contribution 0.42
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.59
SVM decision value 0.60
SVM RNA-class probability 0.795408
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8211117 98 + 20766785
GCCAG--CAGAAGCCAG--AAGGCCAACUAAUUGGCAUUGGCCAAGGUGUUGCGAUGCACAGUG--------GUGAU-CUCUAUCUCCAUUACA--UUAGUUGGCCUACACUC
....(--(....))..(--.((((((((((((((((....))))).((((......))))((((--------(.(((-....))).)))))...--))))))))))).).... ( -34.20)
>DroSec_CAF1 6578 96 + 1
GACAG--CAGAAGCCAG--AAGGCCAACUAAUUGGCAUUGGCCAAGGUGUUGCGAUGCUCAGUG--------GUUAU-CUCUAUCUCCAUUACA--UUAGUUGGCCUA--CUC
....(--(....)).((--.((((((((((((((((....)))))((.(..(.((((((....)--------).)))-).)...).))......--))))))))))).--)). ( -29.00)
>DroSim_CAF1 6501 96 + 1
GCCAG--CAAAAGCCAG--AAGGCCAACUAAUUGGCAUUGGCCAAGGUGUUGCGAUGCACAGUG--------GUUAU-CUCUAUCUCCAUUACA--UUAGUUGGCCUA--CUC
....(--(....)).((--.(((((((((((((((...((((((..((((......))))..))--------)))).-..)))..........)--))))))))))).--)). ( -30.90)
>DroEre_CAF1 6413 94 + 1
GCCCG--GAGAAGCCAG--AAGGCCAACUAAUUGGCAUUGGCCAAGGUGUUGCGAUGCU--GUG--------GCUAU-CUCUAUCUCCAUUACA--UUAGUUGGCCCA--CUC
....(--(.....))..--..(((((((((((((((....)))))((.(..(.(((((.--...--------)).))-).)...).))......--))))))))))..--... ( -29.40)
>DroYak_CAF1 6491 102 + 1
-CCAG--GAGAAGCCAG--AAGGCCAACUAAUUGGCAGUGGCCAAGGUGUUGCGAUGCU--GUGCUGAGAUAGCUAUCCUCUAGCUCCAUUACA--UUAGUUGGCCUG--CUC
-...(--(.....))((--.((((((((((((((((....)))))((.((((.((((((--((......))))).)))...)))).))......--))))))))))).--)). ( -36.50)
>DroAna_CAF1 8728 85 + 1
GCCAGGCCAGGACCCGGAGGAAGCCGGCUAAUUGGCAGUGACCAAGGUGUUGG--------------------------CUUAUCUUCAUUACACAGUUGUUGGCCUU--CUC
...(((((((....)(((((((((((((...((((......))))...)))))--------------------------))).))))).............)))))).--... ( -30.30)
>consensus
GCCAG__CAGAAGCCAG__AAGGCCAACUAAUUGGCAUUGGCCAAGGUGUUGCGAUGCU__GUG________GUUAU_CUCUAUCUCCAUUACA__UUAGUUGGCCUA__CUC
....................((((((((((((((((....)))))((.(...................................).))........)))))))))))...... (-18.76 = -19.18 +   0.42)

alignment

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secondary structure

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Window 7

Location 8,211,117 – 8,211,215
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.00
Mean single sequence MFE -29.69
Consensus MFE -17.99
Energy contribution -18.58
Covariance contribution 0.58
Combinations/Pair 1.15
Mean z-score -1.44
Structure conservation index 0.61
SVM decision value -0.04
SVM RNA-class probability 0.514566
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8211117 98 - 20766785
GAGUGUAGGCCAACUAA--UGUAAUGGAGAUAGAG-AUCAC--------CACUGUGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUG--CUGGC
......(((((((((((--((((.(((.(((....-))).)--------))...))))..........(((((....)))))))))))))))).--(..((....)--)..). ( -33.30)
>DroSec_CAF1 6578 96 - 1
GAG--UAGGCCAACUAA--UGUAAUGGAGAUAGAG-AUAAC--------CACUGAGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUG--CUGUC
.((--.(((((((((((--((..(((....(((.(-.....--------).)))..)))..)).....(((((....)))))))))))))))).--))(((....)--))... ( -28.70)
>DroSim_CAF1 6501 96 - 1
GAG--UAGGCCAACUAA--UGUAAUGGAGAUAGAG-AUAAC--------CACUGUGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUUUG--CUGGC
...--.(((((((((((--((..(((...((((.(-.....--------).)))).)))..)).....(((((....)))))))))))))))).--(..((....)--)..). ( -30.80)
>DroEre_CAF1 6413 94 - 1
GAG--UGGGCCAACUAA--UGUAAUGGAGAUAGAG-AUAGC--------CAC--AGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU--CUGGCUUCUC--CGGGC
...--.(((((((((((--(((..(((..((....-))..)--------)).--.)))..........(((((....))))))))))))))))(--((((.....)--)))). ( -30.00)
>DroYak_CAF1 6491 102 - 1
GAG--CAGGCCAACUAA--UGUAAUGGAGCUAGAGGAUAGCUAUCUCAGCAC--AGCAUCGCAACACCUUGGCCACUGCCAAUUAGUUGGCCUU--CUGGCUUCUC--CUGG-
(((--((((((((((((--(.....(((((((.....)))))......((..--......))....)).((((....)))))))))))))))).--...))))...--....- ( -33.10)
>DroAna_CAF1 8728 85 - 1
GAG--AAGGCCAACAACUGUGUAAUGAAGAUAAG--------------------------CCAACACCUUGGUCACUGCCAAUUAGCCGGCUUCCUCCGGGUCCUGGCCUGGC
(((--.(((((.......((((............--------------------------...)))).(((((....)))))......))))).)))(((((....))))).. ( -22.26)
>consensus
GAG__UAGGCCAACUAA__UGUAAUGGAGAUAGAG_AUAAC________CAC__AGCAUCGCAACACCUUGGCCAAUGCCAAUUAGUUGGCCUU__CUGGCUUCUG__CUGGC
......((((((((((...((..(((..............................)))..)).....(((((....))))).)))))))))).................... (-17.99 = -18.58 +   0.58)

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 10:24:19 2006