Locus 3517

Sequence ID X_DroMel_CAF1
Location 9,435,942 – 9,436,081
Length 139
Max. P 0.806284
window5761 window5762

overview

Window 1

Location 9,435,942 – 9,436,056
Length 114
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 78.17
Mean single sequence MFE -27.60
Consensus MFE -17.06
Energy contribution -17.82
Covariance contribution 0.76
Combinations/Pair 1.17
Mean z-score -1.87
Structure conservation index 0.62
SVM decision value 0.63
SVM RNA-class probability 0.806284
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9435942 114 + 22224390
AAUUUAAAUAUCUUGAAUGCAAAUUUCCACUUUUAAAAUGCUGACAGCGAUUUCGACUCGUCG--ACCGCAUCGGGAAUCCCAAUUUGGAGUUACCCU---UUGGGUAUUAACCCGAUC
..((((((......((((....)))).....)))))).........(((...((((....)))--).)))((((((((((((((...((......)).---))))).)))..)))))). ( -24.90)
>DroSec_CAF1 17522 114 + 1
AAUUUAAAUAUCUUGAAUGCAAAUUUCUACUUUUAAAAUGCUGACAGCGCUUUCGACUCGUCG--ACCGCAUCGGGAAACCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAUC
..((((((......(((.......)))....))))))..((.....))((..((((....)))--)..))((((((....((.....)).(((((((.---..)))))))..)))))). ( -26.70)
>DroEre_CAF1 17944 93 + 1
AAUUUAAAUAUCUUGAA---------------------CGCUGAAAGCAAUUUCAACUCGUCG--ACCGCGUCGGGAAUCCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAUC
............((((.---------------------((.(((((....)))))...)))))--)....((((((..(((......)))(((((((.---..)))))))..)))))). ( -24.60)
>DroYak_CAF1 18466 113 + 1
AAUUUAAAUAUCUUGAAUGCAAAUUUCCACUUUUA-AAUGCUGAAAGCAAUUUCAGCUCGUCG--GCCGCGUUGGGAAUCCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAAC
.(((((((......((((....)))).....))))-)))(((((((....)))))))...(((--((((.((((((...)))))).))).(((((((.---..)))))))...)))).. ( -33.40)
>DroAna_CAF1 15654 118 + 1
AAUUUAAAUAUCUCGAAUGCAAAUAUUCAAUUUAGAAAUGCCAACCGCAAUUUCGACUG-UCUGUGUGGUGAGGGGAAUUCCAAGUGGGAGAUACCCUGCUCCGGGUAUUAACCAGAUC
.........((((.(((((....))))).((((.(((.(.((.((((((....(....)-....))))))...)).).))).))))((..(((((((......)))))))..)))))). ( -28.40)
>consensus
AAUUUAAAUAUCUUGAAUGCAAAUUUCCACUUUUAAAAUGCUGACAGCAAUUUCGACUCGUCG__ACCGCGUCGGGAAUCCCAAUUUGGAGAUACCCU___UUGGGUAUUAACCCGAUC
.......................................((.....))......................((((((..(((......)))(((((((......)))))))..)))))). (-17.06 = -17.82 +   0.76)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,435,981 – 9,436,081
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.74
Mean single sequence MFE -30.66
Consensus MFE -17.92
Energy contribution -19.53
Covariance contribution 1.61
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.58
SVM decision value 0.19
SVM RNA-class probability 0.627841
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9435981 100 + 22224390
GCUGACAGCGAUUUCGACUCGUCG--ACCGCAUCGGGAAUCCCAAUUUGGAGUUACCCU---UUGGGUAUUAACCCGAUCGAAAGUGAGAUGA---------------UUACACAACAAA
.((.((.(((...((((....)))--).)))((((((((((((((...((......)).---))))).)))..)))))).....)).))....---------------............ ( -27.40)
>DroSec_CAF1 17561 100 + 1
GCUGACAGCGCUUUCGACUCGUCG--ACCGCAUCGGGAAACCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAUCGAAAGUGAGAUGA---------------UUACCCAACAAA
.....((.(((((((((...((..--...)).(((((....((.....)).(((((((.---..)))))))..))))))))))))))...)).---------------............ ( -29.20)
>DroEre_CAF1 17962 100 + 1
GCUGAAAGCAAUUUCAACUCGUCG--ACCGCGUCGGGAAUCCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAUCGAAAGUCAGAUGA---------------UUACACGACAAA
..(((((....)))))..((((((--((..(((((((..(((......)))(((((((.---..)))))))..))))).))...))).)))))---------------............ ( -31.70)
>DroYak_CAF1 18504 100 + 1
GCUGAAAGCAAUUUCAGCUCGUCG--GCCGCGUUGGGAAUCCCAAUUUGGAGAUACCCU---UUGGGUAUUAACCCGAACAAAAGUGACAUGA---------------UUACACAAAGAA
(((((((....)))))))((.(((--((((.((((((...)))))).))).(((((((.---..)))))))...))))......((((.....---------------)))).....)). ( -32.60)
>DroAna_CAF1 15693 118 + 1
GCCAACCGCAAUUUCGACUG-UCUGUGUGGUGAGGGGAAUUCCAAGUGGGAGAUACCCUGCUCCGGGUAUUAACCAGAUCGAGAGUGACU-GAGACUGGGACUGGGACUGGAACUACAUA
.((.((((((....(....)-....))))))...))...(((((.(..((......))..)(((.(((.....((((.(((........)-))..)))).))).))).)))))....... ( -32.40)
>consensus
GCUGACAGCAAUUUCGACUCGUCG__ACCGCGUCGGGAAUCCCAAUUUGGAGAUACCCU___UUGGGUAUUAACCCGAUCGAAAGUGAGAUGA_______________UUACACAACAAA
((.....)).........(((((........((((((..(((......)))(((((((......)))))))..)))))).........)))))........................... (-17.92 = -19.53 +   1.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:26 2006