Locus 425

Sequence ID X_DroMel_CAF1
Location 1,240,172 – 1,240,271
Length 99
Max. P 0.782152
window653 window654

overview

Window 3

Location 1,240,172 – 1,240,271
Length 99
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 79.46
Mean single sequence MFE -29.03
Consensus MFE -19.12
Energy contribution -20.23
Covariance contribution 1.11
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.66
SVM decision value 0.36
SVM RNA-class probability 0.705381
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1240172 99 + 22224390
CGGGCGGAACGCCG-------AAAUGGA--------AAAUGGGAAAUCGAAAGUGGAAUAU-----GGUUUUCCGUGCGCUCGCACCCAUCAAUUUUCAUCAGCGGCGAGAGAGCUUAA
.((((....(((((-------..(((((--------((..(((((((((...........)-----))))))))((((....)))).......)))))))...))))).....)))).. ( -30.40)
>DroEre_CAF1 7723 98 + 1
--------ACGCCGAAAUGGGAAAUGGA--------AAAUGGGAAAUCGAAAGUGGAAUAU-----GGUUUUCCGUACGCGCGGACCCAUCAAUUUCCAUCAUCGGCGAGAGAGCUUAA
--------.((((((.(((((((.((..--------..(((((...(((...(((...(((-----((....)))))))).))).))))))).)))))))..))))))........... ( -31.70)
>DroYak_CAF1 7733 111 + 1
--------ACACCGAAAUGGAAAAUGGAAAAACGGAAAAUGGGAAAUCGAAAGUGGAAUAUGGAAUGGUUUUCCGUACGCUCGGACCCAUCAAUUUUCAUCAUCGGCGAGAGAGCUUAA
--------.(.((((.(((((((.((......))....(((((...((((..(((...(((((((.....)))))))))))))).)))))...)))))))..)))).)........... ( -25.00)
>consensus
________ACGCCGAAAUGG_AAAUGGA________AAAUGGGAAAUCGAAAGUGGAAUAU_____GGUUUUCCGUACGCUCGGACCCAUCAAUUUUCAUCAUCGGCGAGAGAGCUUAA
.........((((((....((((((.((...........((((....(....).((((.((......)).))))...........)))))).))))))....))))))........... (-19.12 = -20.23 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,240,172 – 1,240,271
Length 99
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 79.46
Mean single sequence MFE -25.51
Consensus MFE -19.29
Energy contribution -20.52
Covariance contribution 1.23
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.76
SVM decision value 0.56
SVM RNA-class probability 0.782152
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1240172 99 - 22224390
UUAAGCUCUCUCGCCGCUGAUGAAAAUUGAUGGGUGCGAGCGCACGGAAAACC-----AUAUUCCACUUUCGAUUUCCCAUUU--------UCCAUUU-------CGGCGUUCCGCCCG
....((.....(((((..((((......(((((((((....))))((((....-----...))))............))))).--------..)))).-------)))))....))... ( -25.80)
>DroEre_CAF1 7723 98 - 1
UUAAGCUCUCUCGCCGAUGAUGGAAAUUGAUGGGUCCGCGCGUACGGAAAACC-----AUAUUCCACUUUCGAUUUCCCAUUU--------UCCAUUUCCCAUUUCGGCGU--------
...........((((((....((((((.((((((....((.....((((....-----...)))).....))....)))))).--------...))))))....)))))).-------- ( -28.40)
>DroYak_CAF1 7733 111 - 1
UUAAGCUCUCUCGCCGAUGAUGAAAAUUGAUGGGUCCGAGCGUACGGAAAACCAUUCCAUAUUCCACUUUCGAUUUCCCAUUUUCCGUUUUUCCAUUUUCCAUUUCGGUGU--------
...........((((((....((((((.((((((..((((.((..((((............)))))).))))....))))))............))))))....)))))).-------- ( -22.32)
>consensus
UUAAGCUCUCUCGCCGAUGAUGAAAAUUGAUGGGUCCGAGCGUACGGAAAACC_____AUAUUCCACUUUCGAUUUCCCAUUU________UCCAUUU_CCAUUUCGGCGU________
...........((((((....((((((.((((((..((((.((..((((............)))))).))))....))))))............))))))....))))))......... (-19.29 = -20.52 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:17 2006