Locus 2028

Sequence ID X_DroMel_CAF1
Location 5,572,559 – 5,572,660
Length 101
Max. P 0.990609
window3301 window3302

overview

Window 1

Location 5,572,559 – 5,572,660
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.83
Mean single sequence MFE -23.80
Consensus MFE -18.24
Energy contribution -17.76
Covariance contribution -0.48
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.77
SVM decision value 2.22
SVM RNA-class probability 0.990609
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5572559 101 + 22224390
-GCCGACCUCC------------GUCUGAUGAAUCCAAGUUCAUUUCCAAAGUGCAUUACUUGGUUGCCCCAUUAAG---ACGGGCA--AGAAGUUGAACAACUUCCAAUUAUCAU-CAU
-...(((....------------)))((((((..((((((.((((.....))))....))))))((((((.......---..)))))--)((((((....))))))......))))-)). ( -27.20)
>DroSec_CAF1 5399 92 + 1
-GCCGAC-----------------------GCAUCCAAGUUCACUUCCCAAGUGCAUUACUUGGUUGCCCCUUGCAG---UUGGGCAGAAGAAGUUGAACAACUUCCAAUUAUCAU-CAU
-((....-----------------------))......((((((((((((((((...)))))))((((((.......---..))))))..)))).)))))................-... ( -24.00)
>DroSim_CAF1 5480 92 + 1
-GCCGAC-----------------------GCAUCCAAGUUCACUUCCCAAGUGCAUUACUUGGUUGCCCCUUUCAG---AUGGGCAGAAGAAGUUGAACAACUUCCAAUUAUCAU-CAU
-......-----------------------(((.((((((.((((.....))))....)))))).)))........(---((((......((((((....))))))......))))-).. ( -24.80)
>DroEre_CAF1 5740 110 + 1
-GGCCACCCACAGUCUACAUAGAGUCUGACGAAUCCAAGUUCACUUC-AAAGUGCAUUGCUUAGUUGGCCCAUUAAA---UCGGCCA--AGAAGUUC-ACAACUUCCA-UUAUUAU-CAU
-((((.....(((.((......)).))).(((....((((.((((..-..))))....))))..)))..........---..)))).--.(((((..-...)))))..-.......-... ( -20.70)
>DroYak_CAF1 5700 113 + 1
UCGACCUCCAGAGUCUAC----AGUCUAACGAAUCCAAGUUCACUUC-AAAGUGCAUUGCUUAGUUGGCCCAUUGAAUCAUCGGCCA--AGAAGUUGAACAACUUCCAAUUAUUAUCCAU
..((((....).)))...----..((....))......(((((((((-.((((.....))))..((((((.((......)).)))))--))))).))))).................... ( -22.30)
>consensus
_GCCGACC_______________GUCU_A_GAAUCCAAGUUCACUUCCAAAGUGCAUUACUUGGUUGCCCCAUUAAG___UCGGGCA__AGAAGUUGAACAACUUCCAAUUAUCAU_CAU
..................................((((((.((((.....))))....)))))).(((((............)))))...((((((....)))))).............. (-18.24 = -17.76 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,572,559 – 5,572,660
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.83
Mean single sequence MFE -27.78
Consensus MFE -20.88
Energy contribution -20.76
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.09
Structure conservation index 0.75
SVM decision value 0.81
SVM RNA-class probability 0.855753
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5572559 101 - 22224390
AUG-AUGAUAAUUGGAAGUUGUUCAACUUCU--UGCCCGU---CUUAAUGGGGCAACCAAGUAAUGCACUUUGGAAAUGAACUUGGAUUCAUCAGAC------------GGAGGUCGGC-
.((-((((.....(((((((....)))))))--(((((..---.......))))).((((((.((...........))..))))))..))))))(((------------....)))...- ( -27.90)
>DroSec_CAF1 5399 92 - 1
AUG-AUGAUAAUUGGAAGUUGUUCAACUUCUUCUGCCCAA---CUGCAAGGGGCAACCAAGUAAUGCACUUGGGAAGUGAACUUGGAUGC-----------------------GUCGGC-
.((-(((...(((.((....(((((.((((...(((((..---.......))))).((((((.....))))))))))))))))).))).)-----------------------))))..- ( -28.60)
>DroSim_CAF1 5480 92 - 1
AUG-AUGAUAAUUGGAAGUUGUUCAACUUCUUCUGCCCAU---CUGAAAGGGGCAACCAAGUAAUGCACUUGGGAAGUGAACUUGGAUGC-----------------------GUCGGC-
.((-(((...(((.((....(((((.((((...(((((..---.......))))).((((((.....))))))))))))))))).))).)-----------------------))))..- ( -28.60)
>DroEre_CAF1 5740 110 - 1
AUG-AUAAUAA-UGGAAGUUGU-GAACUUCU--UGGCCGA---UUUAAUGGGCCAACUAAGCAAUGCACUUU-GAAGUGAACUUGGAUUCGUCAGACUCUAUGUAGACUGUGGGUGGCC-
...-.......-.((((((...-..))))))--(((((.(---(...)).)))))...........(((((.-..(((..((.((((.((....)).)))).))..)))..)))))...- ( -25.30)
>DroYak_CAF1 5700 113 - 1
AUGGAUAAUAAUUGGAAGUUGUUCAACUUCU--UGGCCGAUGAUUCAAUGGGCCAACUAAGCAAUGCACUUU-GAAGUGAACUUGGAUUCGUUAGACU----GUAGACUCUGGAGGUCGA
((((((.......(((((((....)))))))--(((((.((......)).))))).(((((.....((((..-..))))..)))))))))))..((((----.(((...)))..)))).. ( -28.50)
>consensus
AUG_AUGAUAAUUGGAAGUUGUUCAACUUCU__UGCCCGA___CUGAAUGGGGCAACCAAGUAAUGCACUUUGGAAGUGAACUUGGAUUC_U_AGAC_______________GGUCGGC_
.............(((((((....)))))))..(((((............))))).((((((....((((.....)))).)))))).................................. (-20.88 = -20.76 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:33 2006