Locus 254

Sequence ID 3L_DroMel_CAF1
Location 700,232 – 700,351
Length 119
Max. P 0.984076
window380 window381 window382

overview

Window 0

Location 700,232 – 700,324
Length 92
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 81.70
Mean single sequence MFE -33.33
Consensus MFE -15.72
Energy contribution -18.06
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -3.74
Structure conservation index 0.47
SVM decision value 1.15
SVM RNA-class probability 0.922681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 700232 92 + 23771897
UGGAUGGACUGCGGCG-U---GGAUG-------CCAUAUGUCAACG------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUA
....((((((((((((-(---.(((.-------......))).)))------))))...(((((((((((....)))))))).))).......)))))).......... ( -37.80)
>DroSec_CAF1 55837 81 + 1
UG-----------GCG-U---GGAUG-------CCAUAUGUCAACG------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUA
.(-----------(((-(---.(((.-------......))).)))------)).....(((((((((((....)))))))).)))(((......)))........... ( -25.40)
>DroSim_CAF1 56123 92 + 1
UGGAUGGACUGCGGCG-U---GGAUG-------CCAUAUGUCAACG------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUA
....((((((((((((-(---.(((.-------......))).)))------))))...(((((((((((....)))))))).))).......)))))).......... ( -37.80)
>DroEre_CAF1 57914 92 + 1
UGGAUGGACUGCGGAG-U---AGAUG-------CCAUAUGUCAACG------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUA
....((((((((((.(-(---.(((.-------......))).)).------))))...(((((((((((....)))))))).))).......)))))).......... ( -32.10)
>DroWil_CAF1 41338 103 + 1
UGGCCAGUGUGUUGCU-AUGCCAAUGCAUACAUACAUAUGUCAACGG-----GGGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGAGAAAUCAGUCCAAUUAAAAAUA
((((..((((((((.(-((((....))))))).))))))))))....-----((((....((((((((((....)))))))).))((....)).))))........... ( -33.00)
>DroAna_CAF1 57655 100 + 1
--ACUGGACUACGGCGGC---GGAUC----GCCGCAUAUGUCAACGUUGGUGCUGCGCACGCGCAGAUACAAAUGUAUCUAUAGCGGGAAAUCAGUCCAAUUAAAAAUA
--..((((((...(((((---(...)----))))).........(((((((((.......))))((((((....)))))).))))).......)))))).......... ( -33.90)
>consensus
UGGAUGGACUGCGGCG_U___GGAUG_______CCAUAUGUCAACG______CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUA
....(((((((...........(((..............))).................(((((((((((....)))))))).)))......))))))).......... (-15.72 = -18.06 +   2.33) 

alignment

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secondary structure

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dotplot

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Window 1

Location 700,232 – 700,324
Length 92
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 81.70
Mean single sequence MFE -27.73
Consensus MFE -16.07
Energy contribution -17.10
Covariance contribution 1.03
Combinations/Pair 1.20
Mean z-score -2.53
Structure conservation index 0.58
SVM decision value 0.54
SVM RNA-class probability 0.773154
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 700232 92 - 23771897
UAUUUUUAAUUGGACUGAUUUCCCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCAG------CGUUGACAUAUGG-------CAUCC---A-CGCCGCAGUCCAUCCA
..........(((((((......((((..((((((....))))))(((....)))))------)).........((-------(....---.-.))).))))))).... ( -30.50)
>DroSec_CAF1 55837 81 - 1
UAUUUUUAAUUGGACUGAUUUCCCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCAG------CGUUGACAUAUGG-------CAUCC---A-CGC-----------CA
...........(((......)))((((..((((((....))))))(((....)))))------))........(((-------(....---.-.))-----------)) ( -20.80)
>DroSim_CAF1 56123 92 - 1
UAUUUUUAAUUGGACUGAUUUCCCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCAG------CGUUGACAUAUGG-------CAUCC---A-CGCCGCAGUCCAUCCA
..........(((((((......((((..((((((....))))))(((....)))))------)).........((-------(....---.-.))).))))))).... ( -30.50)
>DroEre_CAF1 57914 92 - 1
UAUUUUUAAUUGGACUGAUUUCCCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCAG------CGUUGACAUAUGG-------CAUCU---A-CUCCGCAGUCCAUCCA
..........(((((((......((((..((((((....))))))(((....)))))------)).........((-------.....---.-..)).))))))).... ( -25.90)
>DroWil_CAF1 41338 103 - 1
UAUUUUUAAUUGGACUGAUUUCUCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCCC-----CCGUUGACAUAUGUAUGUAUGCAUUGGCAU-AGCAACACACUGGCCA
..........(((.((.......(((..(((((((....))))))).)))(((....-----(((.((.(((((....))))))).)))...-.))).......))))) ( -24.50)
>DroAna_CAF1 57655 100 - 1
UAUUUUUAAUUGGACUGAUUUCCCGCUAUAGAUACAUUUGUAUCUGCGCGUGCGCAGCACCAACGUUGACAUAUGCGGC----GAUCC---GCCGCCGUAGUCCAGU--
........(((((((((.......(((..((((((....))))))(((....))))))................(((((----(...)---)))))..)))))))))-- ( -34.20)
>consensus
UAUUUUUAAUUGGACUGAUUUCCCGCUACAGAUACAUUUGUAUCUGCGCGUGCGCAG______CGUUGACAUAUGG_______CAUCC___A_CGCCGCAGUCCAUCCA
..........(((((((......(((..(((((((....))))))).))).............(((......))).......................))))))).... (-16.07 = -17.10 +   1.03) 

alignment

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secondary structure

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dotplot

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Window 2

Location 700,261 – 700,351
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.29
Mean single sequence MFE -27.47
Consensus MFE -17.55
Energy contribution -17.88
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.64
SVM decision value 1.96
SVM RNA-class probability 0.984076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 700261 90 + 23771897
UCAACG-----------------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGCAACG-----GCGGACCGUUCGG--------
....((-----------------(((.((((((((((((((....)))))))).)).(((......))).................))))..))-----)))..((....))-------- ( -29.00)
>DroPse_CAF1 63879 120 + 1
UCAACGAGGAGAGCUACGGUGCGGCGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGGAACUACUAUGCGGAACGUUCCACAACACAC
............(((((.(((((.......)))))((((((....))))))))))).(((......))).................(((((((.............)))))))....... ( -33.42)
>DroWil_CAF1 41377 80 + 1
UCAACGG----------------GGGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGAGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGGAAC-------------GUU-----------
..((((.----------------((((....((((((((((....)))))))).))((....)).)))).((((....))))..........)-------------)))----------- ( -22.10)
>DroYak_CAF1 59935 90 + 1
UCAACG-----------------CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGCAACU-----GCGGACCGUUCGG--------
....((-----------------((((((.(((((((((((....)))))))).)))(((......))).................)))))...-----)))..((....))-------- ( -28.00)
>DroAna_CAF1 57686 84 + 1
UCAACGU---------UGGUG--CUGCGCACGCGCAGAUACAAAUGUAUCUAUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGGAACU-----G--------------------
.....((---------(((.(--(((..(.(((..((((((....))))))...))).)....)))))))))......................-----.-------------------- ( -18.90)
>DroPer_CAF1 68974 120 + 1
UCAACGAGGAGAGCUACGGUGCGGCGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGGAACUACUAUGCGGAACGUUCCACAACACAC
............(((((.(((((.......)))))((((((....))))))))))).(((......))).................(((((((.............)))))))....... ( -33.42)
>consensus
UCAACG_________________CUGCGCACGCGCAGAUACAAAUGUAUCUGUAGCGGGAAAUCAGUCCAAUUAAAAAUAAUAAAGGUGGAACU_____GCGGA_CGUUC__________
..........................(((.(((((((((((....)))))))).)))(((......))).................)))............................... (-17.55 = -17.88 +   0.33) 

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 09:37:35 2006