Locus 4063

Sequence ID 3R_DroMel_CAF1
Location 11,069,020 – 11,069,136
Length 116
Max. P 0.990537
window6511 window6512

overview

Window 1

Location 11,069,020 – 11,069,136
Length 116
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.07
Mean single sequence MFE -26.62
Consensus MFE -12.89
Energy contribution -13.01
Covariance contribution 0.12
Combinations/Pair 1.30
Mean z-score -1.79
Structure conservation index 0.48
SVM decision value 0.20
SVM RNA-class probability 0.632538
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11069020 116 + 27905053
UUUAUUUUGAGUGCCAUUGCUCUUUUGCUGGAAUAUUCCAGCUUGGGAAAAAUGUGAGGCUUCCCCCCCCCCC-ACACAACCACACAAAAAUGCGUGCAUGU-CUG-AUCAUUUAAUUU
......(((((((((.(..(((((..((((((....))))))..)))).....)..))))............(-(.(((..(((.((....)).)))..)))-.))-...))))))... ( -24.80)
>DroSec_CAF1 12739 102 + 1
UUUAUUUUGAAUGCCAUUGCUCUUUUGCUGGAAUAUUCCAGUUUUGGAAAAAUGUGCGGCUUCC-------CC-ACGCAACCACACAAACAUGCGUGCAUGUUCCG-AUCA--------
.......(((..((((((..(((...((((((....))))))...)))..)))).))((.....-------.(-(((((............))))))......)).-.)))-------- ( -25.30)
>DroSim_CAF1 12744 110 + 1
UUUAUUUUGAGUGCCAUUGCUCUUUUGCUGGAAUAUUCCAGUUUUGGAAAAAUGUGCGGCUUCC-------CC-ACGCAACCACACAAACAUGCGUGCAUGUUCCG-AUCAUUUAAUUA
.......((((((...(((((((...((((((....))))))...))).....(((.((....)-------))-))))))...))).((((((....))))))...-.)))........ ( -26.60)
>DroYak_CAF1 12686 109 + 1
UUUAUUUGGAGUGCCAUUGCACUUCGGUUGGAAUAUUCCAGUUUCGAAAAAAUGUGCGGCUUCC-------CC-ACUCAAACACAC--ACAUGCGUGCAUGUGCUGGAAUAAUUAAUUA
((((.(((((((((....))))))))).)))).((((((((............(((.((....)-------))-)).........(--(((((....))))))))))))))........ ( -31.80)
>DroAna_CAF1 12417 100 + 1
UUUAUUUAAAGCGUCG-UGUUCUUUUCCUGGAAUAUUCCAGAGGGGGAAAAUUUUGCGGCUUCC-------CUGACGCACUCACACAUAC--GCAUACCUAC--UCGAACAC-------
..........((((.(-((((((((..(((((....)))))..)))))......((((.(....-------..).))))...))))..))--))........--........------- ( -24.60)
>consensus
UUUAUUUUGAGUGCCAUUGCUCUUUUGCUGGAAUAUUCCAGUUUGGGAAAAAUGUGCGGCUUCC_______CC_ACGCAACCACACAAACAUGCGUGCAUGU_CUG_AUCAUUUAAUU_
..........((((...((((((...((((((....))))))...)))......((((.................)))).............))).))))................... (-12.89 = -13.01 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,069,020 – 11,069,136
Length 116
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 75.07
Mean single sequence MFE -31.54
Consensus MFE -15.88
Energy contribution -16.68
Covariance contribution 0.80
Combinations/Pair 1.29
Mean z-score -2.42
Structure conservation index 0.50
SVM decision value 2.22
SVM RNA-class probability 0.990537
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11069020 116 - 27905053
AAAUUAAAUGAU-CAG-ACAUGCACGCAUUUUUGUGUGGUUGUGU-GGGGGGGGGGGAAGCCUCACAUUUUUCCCAAGCUGGAAUAUUCCAGCAAAAGAGCAAUGGCACUCAAAAUAAA
...........(-((.-(((..((((((....))))))..))).)-))((((((..(((........)))..)))..((((((....))))))......((....)).)))........ ( -35.60)
>DroSec_CAF1 12739 102 - 1
--------UGAU-CGGAACAUGCACGCAUGUUUGUGUGGUUGCGU-GG-------GGAAGCCGCACAUUUUUCCAAAACUGGAAUAUUCCAGCAAAAGAGCAAUGGCAUUCAAAAUAAA
--------(((.-..(((((((....)))))))((((.(((((((-((-------(....)).)))............(((((....))))).......))))).)))))))....... ( -30.80)
>DroSim_CAF1 12744 110 - 1
UAAUUAAAUGAU-CGGAACAUGCACGCAUGUUUGUGUGGUUGCGU-GG-------GGAAGCCGCACAUUUUUCCAAAACUGGAAUAUUCCAGCAAAAGAGCAAUGGCACUCAAAAUAAA
........(((.-..(((((((....)))))))((((.(((((((-((-------(....)).)))............(((((....))))).......))))).)))))))....... ( -33.20)
>DroYak_CAF1 12686 109 - 1
UAAUUAAUUAUUCCAGCACAUGCACGCAUGU--GUGUGUUUGAGU-GG-------GGAAGCCGCACAUUUUUUCGAAACUGGAAUAUUCCAACCGAAGUGCAAUGGCACUCCAAAUAAA
........((((((((..((.((((((....--)))))).)).((-((-------(....)).)))............))))))))........(.(((((....))))).)....... ( -31.50)
>DroAna_CAF1 12417 100 - 1
-------GUGUUCGA--GUAGGUAUGC--GUAUGUGUGAGUGCGUCAG-------GGAAGCCGCAAAAUUUUCCCCCUCUGGAAUAUUCCAGGAAAAGAACA-CGACGCUUUAAAUAAA
-------((((((..--...((...((--((((......))))))..(-------(((((.........))))))))((((((....))))))....)))))-)............... ( -26.60)
>consensus
_AAUUAAAUGAU_CAG_ACAUGCACGCAUGUUUGUGUGGUUGCGU_GG_______GGAAGCCGCACAUUUUUCCAAAACUGGAAUAUUCCAGCAAAAGAGCAAUGGCACUCAAAAUAAA
.................(((((....)))))..((((.(((((............(((((.........)))))....(((((....))))).......))))).)))).......... (-15.88 = -16.68 +   0.80)

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 11:17:14 2006