Locus 5959

Sequence ID 2R_DroMel_CAF1
Location 18,777,302 – 18,777,411
Length 109
Max. P 0.845507
window9559 window9560

overview

Window 9

Location 18,777,302 – 18,777,411
Length 109
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 81.20
Mean single sequence MFE -25.60
Consensus MFE -18.82
Energy contribution -18.98
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -1.76
Structure conservation index 0.74
SVM decision value 0.52
SVM RNA-class probability 0.766063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18777302 109 + 20766785
UGCAUUUUGUUAAGCAAAAAAUUAAAUAACAGCACCCACACACAC--------ACACACACUCGUGGCCAGAGGGGCGGUAAGUGCUAUUAUUUGUUAUUUGGUAAACGCAACAAAU
(((.(((((.....))))).(((((((((((((((((........--------.(((......)))(((.....)))))...)))).......)))))))))))....)))...... ( -24.51)
>DroSec_CAF1 140039 113 + 1
UGCAUUUUGUUAAGCAAAAAAUUAAAUAACAGCUCCCACACACACAAACACA----CACACUCGCGCCCAGAGGGGCGGUAAGUGCUAUUAUUUGUUAUUUGGUAAACGCAACAAAU
(((.(((((.....))))).((((((((((((......).............----..((((..(((((....)))).)..))))........)))))))))))....)))...... ( -24.70)
>DroEre_CAF1 140954 113 + 1
UGCAUUUUGUUAAACAAAAAAUUAAAUAACAGCCCCCGCACACACACAC----ACACAAAUACGCGGCCCGAGGGGCGGUAAGUGCUAUUAUUUGUUGUUUGGUAAAUGCAACAAAU
(((((((.(..((((((.....(((((((.(((...(((..........----..........)))((((...)))).......))).)))))))))))))..))))))))...... ( -24.95)
>DroYak_CAF1 142518 100 + 1
UGCAUUUUGUUAAACAAAAAAUUAAAUAAC-------------ACACAC----AUACAGACUCGCGUCCCGAGGGGCGGUAAGUGCUAUUAUUUGUUGUUUGGUAAAUGCAACAAAU
(((((((.(..((((((.((((..((((.(-------------((...(----.....).....(((((....)))))....))).)))))))).))))))..))))))))...... ( -23.40)
>DroAna_CAF1 139341 114 + 1
UGCAUUUUGUUGAACAAAAAAUUAAAUAACAGCUCCCACACACACGC-CGCAUGCCGCAGGACCCGCCUCGAGGGGCGGUAAGUGCUAUUAUUUGUUAUUUGGUAAAUGCAACA--U
(((((((((.....))))).((((((((((((......(((.....(-(((.....)).))..((((((....))))))...))).......))))))))))))...))))...--. ( -30.42)
>consensus
UGCAUUUUGUUAAACAAAAAAUUAAAUAACAGCUCCCACACACACACAC____ACACAAACUCGCGCCCCGAGGGGCGGUAAGUGCUAUUAUUUGUUAUUUGGUAAAUGCAACAAAU
(((.(((((.....))))).((((((((((((................................(((((....)))))((((......))))))))))))))))....)))...... (-18.82 = -18.98 +   0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,777,302 – 18,777,411
Length 109
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 81.20
Mean single sequence MFE -32.22
Consensus MFE -13.10
Energy contribution -15.86
Covariance contribution 2.76
Combinations/Pair 1.09
Mean z-score -2.59
Structure conservation index 0.41
SVM decision value 0.77
SVM RNA-class probability 0.845507
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18777302 109 - 20766785
AUUUGUUGCGUUUACCAAAUAACAAAUAAUAGCACUUACCGCCCCUCUGGCCACGAGUGUGUGU--------GUGUGUGUGGGUGCUGUUAUUUAAUUUUUUGCUUAACAAAAUGCA
.(((((((((((........)))((((((((((((((((((((.....)))((((......)))--------)...).))))))))))))))))........))..))))))..... ( -29.80)
>DroSec_CAF1 140039 113 - 1
AUUUGUUGCGUUUACCAAAUAACAAAUAAUAGCACUUACCGCCCCUCUGGGCGCGAGUGUG----UGUGUUUGUGUGUGUGGGAGCUGUUAUUUAAUUUUUUGCUUAACAAAAUGCA
......(((((((.(((....(((((((...((((((..(((((....))))).)))))).----..))))))).....)))....(((((..(((....)))..)))))))))))) ( -35.80)
>DroEre_CAF1 140954 113 - 1
AUUUGUUGCAUUUACCAAACAACAAAUAAUAGCACUUACCGCCCCUCGGGCCGCGUAUUUGUGU----GUGUGUGUGUGCGGGGGCUGUUAUUUAAUUUUUUGUUUAACAAAAUGCA
......(((((((...((((((.(((((((((((......(((((.((.(((((((((......----))))))).)).))))))))))))))..)))).))))))....))))))) ( -34.10)
>DroYak_CAF1 142518 100 - 1
AUUUGUUGCAUUUACCAAACAACAAAUAAUAGCACUUACCGCCCCUCGGGACGCGAGUCUGUAU----GUGUGU-------------GUUAUUUAAUUUUUUGUUUAACAAAAUGCA
......(((((((...((((((.((((((((((((...(((.....)))(((....))).....----....))-------------))))))..)))).))))))....))))))) ( -25.10)
>DroAna_CAF1 139341 114 - 1
A--UGUUGCAUUUACCAAAUAACAAAUAAUAGCACUUACCGCCCCUCGAGGCGGGUCCUGCGGCAUGCG-GCGUGUGUGUGGGAGCUGUUAUUUAAUUUUUUGUUCAACAAAAUGCA
.--...(((((((..........((((((((((.....(((((......))))).(((..((.(((((.-..)))))))..))))))))))))).......((.....))))))))) ( -36.30)
>consensus
AUUUGUUGCAUUUACCAAAUAACAAAUAAUAGCACUUACCGCCCCUCGGGCCGCGAGUGUGUGU____GUGUGUGUGUGUGGGAGCUGUUAUUUAAUUUUUUGUUUAACAAAAUGCA
......(((((((..........((((((((((.((((((((((....)).(((......)))...........))).))))).)))))))))).......((.....))))))))) (-13.10 = -15.86 +   2.76)

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 11:59:03 2006