Locus 1379

Sequence ID 3R_DroMel_CAF1
Location 4,021,462 – 4,021,592
Length 130
Max. P 0.961348
window2273 window2274

overview

Window 3

Location 4,021,462 – 4,021,567
Length 105
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 93.28
Mean single sequence MFE -27.60
Consensus MFE -23.14
Energy contribution -23.10
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -1.87
Structure conservation index 0.84
SVM decision value 1.53
SVM RNA-class probability 0.961348
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4021462 105 - 27905053
AUGACAGCCAAAAUGGUGCAAAAGGAGAAACUCCAGUCAACUGGGCCAUGGGCGUAGUUAAAAUGCUUCAAGG-GGUGGGGUUAGAUAAUUUAGAUAUGCCAGAUA
.((((.(((.....)))......((((...)))).)))).(((((((...)))..(((((....((((((...-..))))))....)))))........))))... ( -24.20)
>DroSec_CAF1 27028 105 - 1
AUGACAGCCAAAAUGGCGCAAAAGGAGAAACUCCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGCUUCUAGG-GGUGGGGUUAGAUAAUUAAGAUAUGCCAGAUA
......(((...(((((.(....((((...))))((....))).))))).)))(((.......))).(((.((-.(((.((((....))))....))).))))).. ( -27.20)
>DroSim_CAF1 27595 105 - 1
AUGACAGCCAAAAUGGCGCAAAAGGAGAAACUCCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGCUUCUAGG-GGUGGGGUUAGAUAAUUAAGAUAUGCUAGAUA
......(((...(((((.(....((((...))))((....))).))))).)))(((.......))).(((((.-(.(..((((....))))..)...).))))).. ( -26.50)
>DroEre_CAF1 10042 106 - 1
AUGACAGCCAAAAUGGCGCAAAAGGAGAAACUCCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGCUUCCAGGGGGUGGGGCUAGAUAAUUAAGAUAUGCCAGAUA
.((...(((.....))).))...((((...)))).((((((((.(((...))).))))......(((.(((.....))))))...............))))..... ( -28.00)
>DroYak_CAF1 27762 106 - 1
AUGACAGCCAAAAUGGCGCAAAAGGAGAAACUCCAGGCAACUGGGCCAUGGGCGUAGCUAAAAUGCUGCAGGAGAAUGGGGACAGAUAAUUAAGAUAUGCCAGAUA
......(((...(((((.(....((((...))))((....))).))))).)))(((((......))))).......((....))...................... ( -32.10)
>consensus
AUGACAGCCAAAAUGGCGCAAAAGGAGAAACUCCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGCUUCAAGG_GGUGGGGUUAGAUAAUUAAGAUAUGCCAGAUA
.((.(((((...(((((.(....((((...))))((....))).))))).)))...........(((((........)))))...............)).)).... (-23.14 = -23.10 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,021,501 – 4,021,592
Length 91
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -26.22
Consensus MFE -20.85
Energy contribution -21.47
Covariance contribution 0.61
Combinations/Pair 1.14
Mean z-score -2.09
Structure conservation index 0.80
SVM decision value 0.04
SVM RNA-class probability 0.552556
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4021501 91 - 27905053
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGUGCAAAAGGAGAAACU-CCAGUCAACUGGGCCAUGGGCGUAGUUAAAAUGC
(((..((.(((.(.((((....))))).)))..))...))).(((...((((...))-))....(((((.(((...))).)))))....))) ( -23.90)
>DroSec_CAF1 27067 91 - 1
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAAGGAGAAACU-CCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGC
........(((.(.((((....))))).)))(((...(((((.(....((((...))-))((....))).))))).)))............. ( -28.20)
>DroSim_CAF1 27634 91 - 1
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAAGGAGAAACU-CCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGC
........(((.(.((((....))))).)))(((...(((((.(....((((...))-))((....))).))))).)))............. ( -28.20)
>DroEre_CAF1 10082 91 - 1
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAAGGAGAAACU-CCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGC
........(((.(.((((....))))).)))(((...(((((.(....((((...))-))((....))).))))).)))............. ( -28.20)
>DroYak_CAF1 27802 91 - 1
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAAGGAGAAACU-CCAGGCAACUGGGCCAUGGGCGUAGCUAAAAUGC
...(((..(((.(.((((....))))).)))(((...(((((.(....((((...))-))((....))).))))).)))...)))....... ( -29.20)
>DroAna_CAF1 8208 77 - 1
CCAAGUGAUGUGGCUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAACGAGGAGGCACGAGG---AUGUGGCAAGGACG------------
(((.....((((.(((((.(...(.....).(((.....))).......)))))).))))...---...)))........------------ ( -19.60)
>consensus
CCAAGUGAUGUGACUCCUGCAAAGGAUGACAGCCAAAAUGGCGCAAAAGGAGAAACU_CCAGGCAACUGGGCCAUGGGCGUAGUAAAAAUGC
........(((.(.((((....))))).)))(((...(((((.....((......)).((((....))))))))).)))............. (-20.85 = -21.47 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:36 2006