Locus 1413

Sequence ID 3L_DroMel_CAF1
Location 4,114,809 – 4,115,029
Length 220
Max. P 0.757058
window2193 window2194 window2195

overview

Window 3

Location 4,114,809 – 4,114,918
Length 109
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 82.35
Mean single sequence MFE -21.80
Consensus MFE -13.77
Energy contribution -16.27
Covariance contribution 2.50
Combinations/Pair 0.94
Mean z-score -2.12
Structure conservation index 0.63
SVM decision value 0.30
SVM RNA-class probability 0.678771
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4114809 109 - 23771897
GUUUUCAUUGUAAACUUUGAUAUUCUUAAUGGCAAAUAGCUAAUUGUUUUAUCGUUAUGAAGUAGCAAGGCCAUUUUGAGGCAAUUCGA----AGUUUAUAUUUUUGCGCUUA
((......((((((((((((..(((..((((((.....((((....((((((....))))))))))...))))))..))).....))))----)))))))).....))..... ( -26.40)
>DroSec_CAF1 16271 96 - 1
AUAUUCAUUGUAAACUUUGAUAUUCUUAAUGGCAAAUAGCUAAUUGUU---------------AGCAA-GCCAUAUUCAGGCAAUUUGAAGAAAGUUUAUAUU-UUGAGCUUA
...((((.((((((((((..........(((((...((((.....)))---------------)....-))))).(((((.....))))).))))))))))..-.)))).... ( -20.20)
>DroSim_CAF1 16662 97 - 1
AUAUUCAUUGUAAACUUUGAUAUUCUUAAUGGCAAAUAGCUAAUUGUU---------------AGCAAGGCCAUAUUCAGGCAAUUUAAAAAAAGUUUAUAUU-UUGAGCUUA
...((((.((((((((((......(((..((((((........)))))---------------)..)))(((.......))).........))))))))))..-.)))).... ( -18.80)
>consensus
AUAUUCAUUGUAAACUUUGAUAUUCUUAAUGGCAAAUAGCUAAUUGUU_______________AGCAAGGCCAUAUUCAGGCAAUUUGAA_AAAGUUUAUAUU_UUGAGCUUA
...((((.((((((((((...........((((.....)))).((((((((((.....)))))))))).(((.......))).........))))))))))....)))).... (-13.77 = -16.27 +   2.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,114,845 – 4,114,950
Length 105
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 84.08
Mean single sequence MFE -20.02
Consensus MFE -13.98
Energy contribution -14.32
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.70
SVM decision value 0.30
SVM RNA-class probability 0.679516
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4114845 105 + 23771897
UGGCCUUGCUACUUCAUAACGAUAAAACAAUUAGCUAUUUGCCAUUAAGAAUAUCAAAGUUUACAAUGAAAACCUGCUUAAUCAUUGUGAAAUGGGUUU-UUU----CAA
((((...((((....................)))).....))))....(((.(((....((((((((((............))))))))))...)))..-.))----).. ( -17.85)
>DroSec_CAF1 16310 94 + 1
UGGC-UUGCU---------------AACAAUUAGCUAUUUGCCAUUAAGAAUAUCAAAGUUUACAAUGAAUAUCUGCUUACUCAUUGUGAAAUGGUUUUUUUUUUCACAA
((((-..(((---------------(.....)))).....))))..(((((.((((...((((((((((.((......)).)))))))))).)))).)))))........ ( -21.40)
>DroSim_CAF1 16701 94 + 1
UGGCCUUGCU---------------AACAAUUAGCUAUUUGCCAUUAAGAAUAUCAAAGUUUACAAUGAAUAUCUGCUUACUCAUUGUGAAAUGGGUUU-UUUUUCACAA
((((...(((---------------(.....)))).....))))..(((((.(((....((((((((((.((......)).))))))))))...))).)-))))...... ( -20.80)
>consensus
UGGCCUUGCU_______________AACAAUUAGCUAUUUGCCAUUAAGAAUAUCAAAGUUUACAAUGAAUAUCUGCUUACUCAUUGUGAAAUGGGUUU_UUUUUCACAA
((((...(((......................))).....)))).........(((...((((((((((.((......)).)))))))))).)))............... (-13.98 = -14.32 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,114,918 – 4,115,029
Length 111
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.26
Mean single sequence MFE -21.91
Consensus MFE -11.93
Energy contribution -13.49
Covariance contribution 1.56
Combinations/Pair 1.14
Mean z-score -2.09
Structure conservation index 0.54
SVM decision value 0.49
SVM RNA-class probability 0.757058
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4114918 111 + 23771897
CUGCUUAAUCAUUGUGAAAUGGGUUU-UUU----CAACAAUUGAUUGGCUACUAGCUCACUAUCUUUAGUUUCAUGUUAGCCAAUUAUUUGCUUUCAUUUCGCGACAUUUACUAAG
...........((((((((((((...-...----...(((.((((((((((.((....((((....))))....)).)))))))))).)))..))))))))))))........... ( -26.80)
>DroSec_CAF1 16367 116 + 1
CUGCUUACUCAUUGUGAAAUGGUUUUUUUUUUCACAACAAUUGAUUGGCUACUAGCUCACUAUCUUUAUUUUUACGUUAGCCAAUUAUUUGCUUUCAUUUCGCGACAUCUACUAAG
...........(((((((((((...............(((.((((((((((..........................)))))))))).)))...)))))))))))........... ( -20.64)
>DroSim_CAF1 16759 115 + 1
CUGCUUACUCAUUGUGAAAUGGGUUU-UUUUUCACAACAAUUGAUUGGCUACUAGCUCACUAUCUUUAUUUUUACGUUAGCCAAUUAUUUGCUUUCAUUUCGCGACAUCUACUAAG
...........(((((((((((((..-......))..(((.((((((((((..........................)))))))))).)))...)))))))))))........... ( -21.97)
>DroEre_CAF1 16587 111 + 1
C---UUGUGAAUUGCGAAACUGUUU--UCUUUCGCAAAAAUUGAUUGGCGUCUAAUUCACUAUAUUUAUUUUCACAUUAGCCAAUUAUUUGCUUUUAUUUCGAUUCAUAUACUAAG
.---.(((((((((.((((......--..))))(((((...((((((((..............................)))))))))))))........)))))))))....... ( -20.81)
>DroYak_CAF1 16819 104 + 1
C---UUGUGAAUUGUGCAAUUGUUU--UCUUUCGCAAAAAUUGAUUGGCUCCUAGUUAACGAUAUUUACU------UUAGCCAGUUAUUUGCUUUCAUUUCGGGU-GUAUACUAAG
.---........((((((.(((...--......(((((...(((((((((...(((...........)))------..))))))))))))))........))).)-)))))..... ( -19.33)
>consensus
CUGCUUACUCAUUGUGAAAUGGUUUU_UUUUUCACAACAAUUGAUUGGCUACUAGCUCACUAUCUUUAUUUUCACGUUAGCCAAUUAUUUGCUUUCAUUUCGCGACAUAUACUAAG
...........((((((((..........))))))))(((.((((((((((..........................)))))))))).)))......................... (-11.93 = -13.49 +   1.56)

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 10:06:51 2006