Locus 1493

Sequence ID 3L_DroMel_CAF1
Location 4,330,676 – 4,330,897
Length 221
Max. P 0.996344
window2324 window2325 window2326

overview

Window 4

Location 4,330,676 – 4,330,788
Length 112
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 95.41
Mean single sequence MFE -38.26
Consensus MFE -30.20
Energy contribution -29.88
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.23
Structure conservation index 0.79
SVM decision value 1.00
SVM RNA-class probability 0.898162
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4330676 112 + 23771897
CCCAGAAC--CAGCGAUUGGAUAAAGCUGCCCCGCUCUAUAAAUAGAGCCCUGGUCGAGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCUCU-GGCUUU
.......(--(((.((((.((.(((((......((((((....)))))).(((((((.((...(((......)))..)).)))))))......))))))).)))).))-)).... ( -35.70)
>DroSec_CAF1 17179 112 + 1
CCCAGAAC--CAGCGAUUGGAUAAAGCUGCUCCGCUCUAUAAAUAGAGCCCUGGUCGCGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCUCU-GGCUUU
.......(--(((.((((.((.(((((.((((.((((((....))))))..(((((((((...(((......)))..)))))))))))))...))))))).)))).))-)).... ( -42.40)
>DroSim_CAF1 15771 112 + 1
CCCAGAAC--CAGCGAUUGGAUAAAGCUGCCCCGCUCUAUAAAUAGAGCCCUGGCCGAGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCUCU-GGCUUU
.......(--(((.((((.((.(((((......((((((....)))))).(((((((.((...(((......)))..)).)))))))......))))))).)))).))-)).... ( -38.40)
>DroEre_CAF1 17187 112 + 1
CCCAGAAC--CACCGAUUGGAUGAAGCUGCC-CGCUCUAUAAAUAGAGCCCUGGUCGGGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCGCUUUGUUUU
...(((((--...(((((((((((((((...-.((((((....)))))).(((((((.((...(((......)))..)).))))))))))))))...))).)))))....))))) ( -34.10)
>DroYak_CAF1 16370 114 + 1
CCCAGAACAGCAGCGAUUGGAUAAAGCUGCCCCGCUCUAUAAAUAGAGCCCUGGUCGCGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCUCU-GGCUUU
.(((((((.(((((...........)))))...((((((....)))))).((((((((((...(((......)))..))))))))))...............)).)))-)).... ( -40.70)
>consensus
CCCAGAAC__CAGCGAUUGGAUAAAGCUGCCCCGCUCUAUAAAUAGAGCCCUGGUCGAGCCUUAUCAGCCUCGAUCCGCGUGGCCAGAGUUUCGCUUUUCAAGUCUCU_GGCUUU
..............((((.((.(((((......((((((....)))))).(((((((.((...(((......)))..)).)))))))......))))))).)))).......... (-30.20 = -29.88 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,330,676 – 4,330,788
Length 112
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 95.41
Mean single sequence MFE -40.10
Consensus MFE -31.56
Energy contribution -31.60
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.79
SVM decision value 0.17
SVM RNA-class probability 0.614889
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4330676 112 - 23771897
AAAGCC-AGAGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCUCGACCAGGGCUCUAUUUAUAGAGCGGGGCAGCUUUAUCCAAUCGCUG--GUUCUGGG
....((-((((.((.....(((((......((((.((.....)).))))(((((((((.(.((...((((((....))))))..))))))))))))...))))))--))))))). ( -40.90)
>DroSec_CAF1 17179 112 - 1
AAAGCC-AGAGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCGCGACCAGGGCUCUAUUUAUAGAGCGGAGCAGCUUUAUCCAAUCGCUG--GUUCUGGG
....((-((((.((.....(((((......((((.((.....)).))))((((((((((..((...((((((....)))))))).)).))))))))...))))))--))))))). ( -39.70)
>DroSim_CAF1 15771 112 - 1
AAAGCC-AGAGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCUCGGCCAGGGCUCUAUUUAUAGAGCGGGGCAGCUUUAUCCAAUCGCUG--GUUCUGGG
....((-((((.((.....(((((......((((.((.....)).))))(((((((((..(((...((((((....))))))..))))))))))))...))))))--))))))). ( -43.10)
>DroEre_CAF1 17187 112 - 1
AAAACAAAGCGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCCCGACCAGGGCUCUAUUUAUAGAGCG-GGCAGCUUCAUCCAAUCGGUG--GUUCUGGG
....((.(((.(((.((...(((............)))((((.(((((((.......((.....))((((((....)))))).-..)))))))))))..))))).--))).)).. ( -34.40)
>DroYak_CAF1 16370 114 - 1
AAAGCC-AGAGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCGCGACCAGGGCUCUAUUUAUAGAGCGGGGCAGCUUUAUCCAAUCGCUGCUGUUCUGGG
...(((-((((..(((.....)))..)))))))..((((.((((....))))....)))).(((((((((((....))))))..((((((...........))))))..))))). ( -42.40)
>consensus
AAAGCC_AGAGACUUGAAAAGCGAAACUCUGGCCACGCGGAUCGAGGCUGAUAAGGCGCGACCAGGGCUCUAUUUAUAGAGCGGGGCAGCUUUAUCCAAUCGCUG__GUUCUGGG
............((.(((.(((((.......((...))((((.(((((((....((.....))...((((((....))))))....)))))))))))..)))))....))).)). (-31.56 = -31.60 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,330,788 – 4,330,897
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.03
Mean single sequence MFE -21.66
Consensus MFE -12.73
Energy contribution -13.23
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.59
SVM decision value 2.68
SVM RNA-class probability 0.996344
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4330788 109 + 23771897
UUUCCUUUUCUUUUCUUUUUGU-------UUUUCACUCGCUCUCGAGUGGCCAUAAAAAUUUGUUGCAUUUCCGUUGGCUUGUACAUGAAAAUAUGCAGCAACUCUCCU----CUUGCAA
...............(((((((-------...(((((((....)))))))..))))))).(((((((((......((.......)).......))))))))).......----....... ( -20.42)
>DroEre_CAF1 17299 104 + 1
UAUCCAUUUCUUUUCC-----------UUUUCUCGCUCGCUCUCGAGUGGCCAUAAAAAUUUGUUGCAUUUCCGUU-GCUUGUACAAGAAAAUAUGCAGCAACUCUCUUGCAACUU----
................-----------.....(((((((....)))))))............((((((.....(((-(((.(((..........))))))))).....))))))..---- ( -22.80)
>DroYak_CAF1 16484 111 + 1
UUUCCUUUUCUUUUCUUUUUU----CAUUUUUUCACUCGCUCUCGAGUGGCCAUAAAAAUUUGUUGCAUUUCCGUU-GCUUGUACAAGAAAAUAUGCAGCAACUCUCUUGCAACUU----
.....................----.......(((((((....)))))))............((((((.....(((-(((.(((..........))))))))).....))))))..---- ( -23.30)
>DroAna_CAF1 16869 96 + 1
UUUCGCUUCAGCCUCCC-AGGCUAG-UCUUUUUCUCUCUCUGCGGAGUGGCCAUAAAAAUUUGUUGCAUUUCCGUU-GCUUGUACAACAAACUAUGCAG---------------------
....(((..((((....-.))))))-)............((((((((..((.((((....)))).))..))))(((-(......)))).......))))--------------------- ( -20.10)
>consensus
UUUCCUUUUCUUUUCCU_UUG______UUUUUUCACUCGCUCUCGAGUGGCCAUAAAAAUUUGUUGCAUUUCCGUU_GCUUGUACAAGAAAAUAUGCAGCAACUCUCUU____CUU____
................................(((((((....)))))))..........(((((((((........................))))))))).................. (-12.73 = -13.23 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:06 2006