Locus 1113

Sequence ID 3L_DroMel_CAF1
Location 3,262,326 – 3,262,453
Length 127
Max. P 0.720540
window1724 window1725

overview

Window 4

Location 3,262,326 – 3,262,424
Length 98
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 88.34
Mean single sequence MFE -25.55
Consensus MFE -21.48
Energy contribution -22.12
Covariance contribution 0.64
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.84
SVM decision value 0.26
SVM RNA-class probability 0.656373
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3262326 98 - 23771897
AAAAACGAGGUGUGACCGAAUCGGGUC-CCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC---CCCGAAUUACGAAAUUAU
.....((((((((((((((((.(((..-......))))))))))).)))).))))....(((.((((....)))).)))..---.................. ( -27.20)
>DroSec_CAF1 40975 95 - 1
-AAAACGAGGUGUGACCGAAUCGGGUCCCCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC---CCCGAAUUACGAAA---U
-....((((((((((((((((.(((.........))))))))))).)))).))))....(((.((((....)))).)))..---..............---. ( -26.40)
>DroSim_CAF1 43930 97 - 1
--AAACGAGGUGUGACCGAAUCGGGUGCCCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC---CCCGAAUUACGAAAUUAU
--...((((((((((((((((.((((......)))).)))))))).)))).))))....(((.((((....)))).)))..---.................. ( -27.50)
>DroEre_CAF1 42262 95 - 1
---AACGAGGUGUGACCGUAUCGGGUC-CCCAAUUCCAUUUGGCCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC---CCCGAAUUACGAAAUUAU
---..((((((((((((......))))-.((((......))))...)))).))))....(((.((((....)))).)))..---.................. ( -19.00)
>DroYak_CAF1 42542 95 - 1
---AACAAGGUGUGACCGAAUCGGGUA-CCCAAUUCCAUUUGGUCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC---CCCGAAUUACGAAAUUAU
---......((((((((((((.(((..-......))))))))))).))))..(((....(((.((((....)))).)))..---..)))............. ( -21.40)
>DroAna_CAF1 42714 92 - 1
---AAUGAGGUGUGACCGAAUCGGGUC-U----UCCGAUUUGGUCAACCCCCUCG-ACACUGCCCGAAUU-UUGAUUAGGCUUUCUGGCAUUACGAAAUUAU
---..(((((..((((((((((((...-.----.))))))))))))....)))))-....((((.(((..-...........))).))))............ ( -31.82)
>consensus
___AACGAGGUGUGACCGAAUCGGGUC_CCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCUCGAAUUUUUGAUUAGCC___CCCGAAUUACGAAAUUAU
.....((((((((((((((((.((((......)))).)))))))).)))).))))....(((.((((....)))).)))....................... (-21.48 = -22.12 +   0.64) 

alignment

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secondary structure

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dotplot

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Window 5

Location 3,262,361 – 3,262,453
Length 92
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 86.44
Mean single sequence MFE -25.00
Consensus MFE -19.84
Energy contribution -20.32
Covariance contribution 0.47
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.79
SVM decision value 0.40
SVM RNA-class probability 0.720540
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3262361 92 - 23771897
UAUUGAUAUUUUCUGAUUAAAGUGUAAAAAAAAACGAGGUGUGACCGAAUCGGGUC-CCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCU
....................(((((.........((((((((((((((((.(((..-......))))))))))).)))).)))).)))))... ( -27.10)
>DroSec_CAF1 41007 91 - 1
UAUUGAUAUUUUCUGAUUGAAGUUUAAA--AAAACGAGGUGUGACCGAAUCGGGUCCCCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCU
..((((...((((.....)))).)))).--....((((((((((((((((.(((.........))))))))))).)))).))))......... ( -25.70)
>DroSim_CAF1 43965 90 - 1
UAUUGAUAUUUUCUGAUUGAAGUUUAAA---AAACGAGGUGUGACCGAAUCGGGUGCCCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCU
..((((...((((.....)))).)))).---...((((((((((((((((.((((......)))).)))))))).)))).))))......... ( -26.80)
>DroEre_CAF1 42297 87 - 1
UAUUGAUAUUUUCAGAUUGAAGUUUGA-----AACGAGGUGUGACCGUAUCGGGUC-CCCAAUUCCAUUUGGCCAACGCACUCGCACACUGCU
.........((((((((....))))))-----))((((((((((((......))))-.((((......))))...)))).))))......... ( -21.70)
>DroYak_CAF1 42577 87 - 1
UAUUGAUAUUUUCAGAUUGAAGUUUAC-----AACAAGGUGUGACCGAAUCGGGUA-CCCAAUUCCAUUUGGUCAACGCACUCGCACACUGCU
..((((.....))))............-----.....(((((((((((((.(((..-......)))))))))))...((....)))))))... ( -20.40)
>DroAna_CAF1 42751 82 - 1
UAUUGAUACUUUUCAAUUGAAGUUUGG-----AAUGAGGUGUGACCGAAUCGGGUC-U----UCCGAUUUGGUCAACCCCCUCG-ACACUGCC
..((.(.(((((......))))).).)-----).(((((..((((((((((((...-.----.))))))))))))....)))))-........ ( -28.30)
>consensus
UAUUGAUAUUUUCUGAUUGAAGUUUAA_____AACGAGGUGUGACCGAAUCGGGUC_CCCAAUCCCAUUUGGUCAACGCACUCGCACACUGCU
..................................((((((((((((((((.((((......)))).)))))))).)))).))))......... (-19.84 = -20.32 +   0.47) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:22 2006