Locus 4305

Sequence ID X_DroMel_CAF1
Location 11,356,693 – 11,356,831
Length 138
Max. P 0.999375
window7077 window7078 window7079

overview

Window 7

Location 11,356,693 – 11,356,805
Length 112
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 76.61
Mean single sequence MFE -35.60
Consensus MFE -19.01
Energy contribution -20.35
Covariance contribution 1.34
Combinations/Pair 1.20
Mean z-score -3.68
Structure conservation index 0.53
SVM decision value 2.88
SVM RNA-class probability 0.997549
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11356693 112 + 22224390
UGGCAAAACGCGC--GCCGCUCGCGCACAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG-AUCGUGAUCGUGGC-CAUGAUCAUGAUUAUGAUUAUGAUCAUGAUCAUCCACAUGA
(((......((((--(.....)))))............((((((((((((..(((((((-(((((((((((...-.))))))))))))))))))..)))))))))))))))..... ( -48.80)
>DroSec_CAF1 17645 106 + 1
UAGCAAAACGCGC--GCCGCUCGCGCACAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG-AUCGUGAUCGUGGC-CAUGAUCAUGAUU------AUGAUCAUGAUCAUCCACAUGA
.........((((--(.....)))))....(((.....((((((((((((..(((((((-((((((........-)))))))))))))------..))))))))))))....))). ( -41.60)
>DroSim_CAF1 239 94 + 1
UAGCAAAACGCGC--GCCGCUCGCGCACAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG-AUCGUGAUCGUGGC-CAUGAUC------------------AUGAUCAUCCACAUGA
.........((((--(.....))))).........((.(((((((((.(..(((((((.-...)))))))..).-)))))))------------------))..)).......... ( -33.00)
>DroEre_CAF1 21333 100 + 1
UAGCAAAACGCAC--GCCGCUCGCGCGCAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG-AUCGUGAUCGUGGC-CAUGAUCAUGAUC------AUGA------UUAUGAACAUGA
.........((.(--((.....))).))..............(((((.((..(((((((-(((((((((((...-.))))))))))))------))))------))..)).))))) ( -36.40)
>DroYak_CAF1 22608 100 + 1
UAGCAAAACGCGC--GCCGCUUGCGCACAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG-AUCGUGAUCGUGGC-CAUGAUCAUGAUC------AUGA------UCAUGAACAUGA
..((.....))((--((.....))))................(((((.((..(((((((-(((((((((((...-.))))))))))))------))))------))..)).))))) ( -38.60)
>DroMoj_CAF1 28089 94 + 1
UAGCAAAACGCGACAGCCAAAUGC-----GCAUUAGAAGUCAUCAAAAACAUGAUUG-GAAUUGGUAUCG--GCAAAUGAUAGCGGUA------AAAU------AUAUCGAUAU--
..((.....))....(((..((((-----.((.....((((((.......)))))).-....)))))).)--)).........(((((------....------.)))))....-- ( -15.20)
>consensus
UAGCAAAACGCGC__GCCGCUCGCGCACAGCAUUAGAAGUGAUCAUGAUUGCGAUUAUG_AUCGUGAUCGUGGC_CAUGAUCAUGAUC______AUGA______UCAUCCACAUGA
..((....((((.........))))....)).......(((((((((..((((((((((...))))))))))...)))))))))................................ (-19.01 = -20.35 +   1.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,356,731 – 11,356,831
Length 100
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 72.49
Mean single sequence MFE -31.37
Consensus MFE -14.03
Energy contribution -14.87
Covariance contribution 0.84
Combinations/Pair 1.27
Mean z-score -4.13
Structure conservation index 0.45
SVM decision value 3.55
SVM RNA-class probability 0.999375
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11356731 100 + 22224390
GAUCAUGAUUGC---GAUUAUGAUCGUGAUCGUGGCCAUGAUCAUGAUUAUGAUUAUG-AUCAUGAUCAUCCACAUGAUGGAG---UUGUGCCGCAAAAAAAUUAAC
((((((((((..---......))))))))))((((((((((((((((((((....)))-))))))))))((((.....)))).---.)).)))))............ ( -40.40)
>DroSec_CAF1 17683 94 + 1
GAUCAUGAUUGC---GAUUAUGAUCGUGAUCGUGGCCAUGAUCAUGAUU------AUG-AUCAUGAUCAUCCACAUGAUGGAG---UUGUGCCGCAAAAAAAUUAAC
((((((((((..---......))))))))))(((((((((((((((((.------...-))))))))))((((.....)))).---.)).)))))............ ( -37.30)
>DroSim_CAF1 277 82 + 1
GAUCAUGAUUGC---GAUUAUGAUCGUGAUCGUGGCCAUGAUC-------------------AUGAUCAUCCACAUGAUGGAG---UUGUGCCGCAAAAAAAUUAAC
((((((((((..---......))))))))))((((((((.(((-------------------(((........)))))).)..---.)).)))))............ ( -27.10)
>DroEre_CAF1 21371 88 + 1
GAUCAUGAUUGC---GAUUAUGAUCGUGAUCGUGGCCAUGAUCAUGAUC------AUG-A------UUAUGAACAUGAUGGAG---UUGUGCCGCGAAGAAAUUAAC
.((((((.((..---((((((((((((((((((....))))))))))))------)))-)------))..)).))))))((..---.....)).............. ( -31.80)
>DroYak_CAF1 22646 88 + 1
GAUCAUGAUUGC---GAUUAUGAUCGUGAUCGUGGCCAUGAUCAUGAUC------AUG-A------UCAUGAACAUGAUGGAG---UUGUGCCGCGAAGAAAUUAAC
.((((((.((..---((((((((((((((((((....))))))))))))------)))-)------))..)).))))))((..---.....)).............. ( -33.30)
>DroAna_CAF1 12466 92 + 1
AGUCAUUAUCGCCGUGAUUAUGAAUGCGAAUGCGAUUAUGAUUUGGAAA------CUGAAUUAUAAGCA--CACACGACGAGACGAGAGUGCCCGGAAUG-------
.(((....(((.((((.........((....))(.((((((((((....------).))))))))).).--..)))).))))))................------- ( -18.30)
>consensus
GAUCAUGAUUGC___GAUUAUGAUCGUGAUCGUGGCCAUGAUCAUGAUC______AUG_A__AUGAUCAUCCACAUGAUGGAG___UUGUGCCGCAAAAAAAUUAAC
((((((((((.....))))))))))...((((((...((((((.....................))))))...))))))............................ (-14.03 = -14.87 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,356,731 – 11,356,831
Length 100
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 72.49
Mean single sequence MFE -22.42
Consensus MFE -5.08
Energy contribution -6.19
Covariance contribution 1.11
Combinations/Pair 1.20
Mean z-score -2.75
Structure conservation index 0.23
SVM decision value 1.02
SVM RNA-class probability 0.901521
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11356731 100 - 22224390
GUUAAUUUUUUUGCGGCACAA---CUCCAUCAUGUGGAUGAUCAUGAU-CAUAAUCAUAAUCAUGAUCAUGGCCACGAUCACGAUCAUAAUC---GCAAUCAUGAUC
..........(((((((.((.---.(((((...)))))((((((((((-.((....)).)))))))))))))))..(((....)))......---))))........ ( -26.00)
>DroSec_CAF1 17683 94 - 1
GUUAAUUUUUUUGCGGCACAA---CUCCAUCAUGUGGAUGAUCAUGAU-CAU------AAUCAUGAUCAUGGCCACGAUCACGAUCAUAAUC---GCAAUCAUGAUC
..........(((((((.((.---.(((((...)))))((((((((((-...------.)))))))))))))))..(((....)))......---))))........ ( -26.50)
>DroSim_CAF1 277 82 - 1
GUUAAUUUUUUUGCGGCACAA---CUCCAUCAUGUGGAUGAUCAU-------------------GAUCAUGGCCACGAUCACGAUCAUAAUC---GCAAUCAUGAUC
..........((((((.....---.(((((...)))))(((((.(-------------------((((........))))).)))))...))---))))........ ( -20.70)
>DroEre_CAF1 21371 88 - 1
GUUAAUUUCUUCGCGGCACAA---CUCCAUCAUGUUCAUAA------U-CAU------GAUCAUGAUCAUGGCCACGAUCACGAUCAUAAUC---GCAAUCAUGAUC
..........(((.(((.((.---....((((((.((((..------.-.))------)).))))))..))))).)))....((((((.((.---...)).)))))) ( -20.20)
>DroYak_CAF1 22646 88 - 1
GUUAAUUUCUUCGCGGCACAA---CUCCAUCAUGUUCAUGA------U-CAU------GAUCAUGAUCAUGGCCACGAUCACGAUCAUAAUC---GCAAUCAUGAUC
..........(((.(((..((---(........)))(((((------(-(((------....)))))))))))).)))....((((((.((.---...)).)))))) ( -23.50)
>DroAna_CAF1 12466 92 - 1
-------CAUUCCGGGCACUCUCGUCUCGUCGUGUG--UGCUUAUAAUUCAG------UUUCCAAAUCAUAAUCGCAUUCGCAUUCAUAAUCACGGCGAUAAUGACU
-------......((((((.(.((......)).).)--))))).........------........((((.(((((...................))))).)))).. ( -17.61)
>consensus
GUUAAUUUUUUCGCGGCACAA___CUCCAUCAUGUGGAUGAUCAU__U_CAU______AAUCAUGAUCAUGGCCACGAUCACGAUCAUAAUC___GCAAUCAUGAUC
..........(((.(((...........((((((...........................))))))....))).)))....((((((.((.......)).)))))) ( -5.08 =  -6.19 +   1.11)

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 11:21:44 2006