Locus 6231

Sequence ID 2R_DroMel_CAF1
Location 19,581,638 – 19,581,734
Length 96
Max. P 0.993477
window9982 window9983

overview

Window 2

Location 19,581,638 – 19,581,734
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.42
Mean single sequence MFE -28.64
Consensus MFE -15.62
Energy contribution -15.78
Covariance contribution 0.17
Combinations/Pair 1.05
Mean z-score -3.25
Structure conservation index 0.55
SVM decision value 2.16
SVM RNA-class probability 0.989370
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19581638 96 + 20766785
----------AUGGGC------CUGGCCUUCAUAAAU-UGUUAGGCUCAUUGCCAAUCGCAAGUGAGCGAUUUACAAUUAACAAAUA------CCCAGAG-CCCCUCUAUUUAUAGAUAU
----------..((((------((((........(((-(((..(((.....)))((((((......)))))).))))))........------.)))).)-))).((((....))))... ( -27.83)
>DroPse_CAF1 2215 99 + 1
AGAUCGGAUCGUAGAU------CUGGCCUUCAUAAAU-UGUUAGGCUCAUUGCCAAUCGCAAUUGAGCGAUUUACAAUUAAUAAAUA------CAUAC--------UUAUUUAUAGAUUU
((..((((((...)))------)))..)).....(((-(((..(((.....)))((((((......)))))).)))))).(((((((------.....--------.)))))))...... ( -23.00)
>DroEre_CAF1 4339 108 + 1
----------AUGGGCCUGGGCCUGGCCUUCAUAAAU-UGUUAGGCUCAUUGCCAAUCGCAAGUGAGCGAUUUACAAUUAACGAAUAGCCAUGCCCAGAG-CCCCUCUAUUUUUAGAUAU
----------..((((((((((.((((.(((...(((-(((..(((.....)))((((((......)))))).))))))...)))..)))).)))))).)-))).((((....))))... ( -44.60)
>DroYak_CAF1 4338 102 + 1
----------AUGGGCCUGGGCCUGGCCUUCAUAAAU-UGUUAGGCUCAUUGCCAAUCGCAAGUGAGCGAUUUACAAUUAACAAAUA------CCCAGUG-CCCCUCUAUUUAUAGAUAU
----------..(((((((((...(((((.((.....-))..))))).((((..((((((......))))))..)))).........------))))).)-))).((((....))))... ( -32.80)
>DroAna_CAF1 4962 98 + 1
----------AUAGGU------CUGGCCUUCAUAAAUCUGUUAGGCUCAUUGCCAAUCGCAAGUGAGCGAUUUACAAUUAACAAAUA------CCUAGAUACUGGUUUAUUAUUAGAUAU
----------.(((((------..(((((.((......))..))))).((((..((((((......))))))..))))........)------))))....(((((.....))))).... ( -20.60)
>DroPer_CAF1 5050 99 + 1
AGAUCGGAUCGUAGAU------CUGGCCUUCAUAAAU-UGUUAGGCUCAUUGCCAAUCGCAAUUGAGCGAUUUACAAUUAAUAAAUA------CAUAC--------UUAUUUAUAGAUUU
((..((((((...)))------)))..)).....(((-(((..(((.....)))((((((......)))))).)))))).(((((((------.....--------.)))))))...... ( -23.00)
>consensus
__________AUAGGC______CUGGCCUUCAUAAAU_UGUUAGGCUCAUUGCCAAUCGCAAGUGAGCGAUUUACAAUUAACAAAUA______CCCAGAG_CCCCUCUAUUUAUAGAUAU
...........((((.........(((((.((......))..))))).((((..((((((......))))))..))))...............))))....................... (-15.62 = -15.78 +   0.17)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,581,638 – 19,581,734
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.42
Mean single sequence MFE -31.43
Consensus MFE -17.99
Energy contribution -17.60
Covariance contribution -0.39
Combinations/Pair 1.10
Mean z-score -3.72
Structure conservation index 0.57
SVM decision value 2.40
SVM RNA-class probability 0.993477
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19581638 96 - 20766785
AUAUCUAUAAAUAGAGGGG-CUCUGGG------UAUUUGUUAAUUGUAAAUCGCUCACUUGCGAUUGGCAAUGAGCCUAACA-AUUUAUGAAGGCCAG------GCCCAU----------
...((((....)))).(((-(.((((.------..((..(.((((((.((((((......))))))(((.....)))..)))-))).)..))..))))------))))..---------- ( -33.70)
>DroPse_CAF1 2215 99 - 1
AAAUCUAUAAAUAA--------GUAUG------UAUUUAUUAAUUGUAAAUCGCUCAAUUGCGAUUGGCAAUGAGCCUAACA-AUUUAUGAAGGCCAG------AUCUACGAUCCGAUCU
..............--------....(------(.(((((.((((((.((((((......))))))(((.....)))..)))-))).))))).)).((------(((........))))) ( -21.90)
>DroEre_CAF1 4339 108 - 1
AUAUCUAAAAAUAGAGGGG-CUCUGGGCAUGGCUAUUCGUUAAUUGUAAAUCGCUCACUUGCGAUUGGCAAUGAGCCUAACA-AUUUAUGAAGGCCAGGCCCAGGCCCAU----------
...((((....)))).(((-(.((((((.(((((.(((((.((((((.((((((......))))))(((.....)))..)))-))).)))))))))).))))))))))..---------- ( -51.60)
>DroYak_CAF1 4338 102 - 1
AUAUCUAUAAAUAGAGGGG-CACUGGG------UAUUUGUUAAUUGUAAAUCGCUCACUUGCGAUUGGCAAUGAGCCUAACA-AUUUAUGAAGGCCAGGCCCAGGCCCAU----------
...((((....)))).(((-(.(((((------(........(((((.((((((......)))))).)))))(.((((....-........)))))..))))))))))..---------- ( -37.60)
>DroAna_CAF1 4962 98 - 1
AUAUCUAAUAAUAAACCAGUAUCUAGG------UAUUUGUUAAUUGUAAAUCGCUCACUUGCGAUUGGCAAUGAGCCUAACAGAUUUAUGAAGGCCAG------ACCUAU----------
.......................((((------(........(((((.((((((......)))))).)))))(.((((..((......)).)))))..------))))).---------- ( -21.90)
>DroPer_CAF1 5050 99 - 1
AAAUCUAUAAAUAA--------GUAUG------UAUUUAUUAAUUGUAAAUCGCUCAAUUGCGAUUGGCAAUGAGCCUAACA-AUUUAUGAAGGCCAG------AUCUACGAUCCGAUCU
..............--------....(------(.(((((.((((((.((((((......))))))(((.....)))..)))-))).))))).)).((------(((........))))) ( -21.90)
>consensus
AUAUCUAUAAAUAAAGGGG_CUCUAGG______UAUUUGUUAAUUGUAAAUCGCUCACUUGCGAUUGGCAAUGAGCCUAACA_AUUUAUGAAGGCCAG______ACCCAU__________
.......................((((...............(((((.((((((......)))))).)))))(.((((.............))))).........))))........... (-17.99 = -17.60 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:15 2006