Locus 4577

Sequence ID X_DroMel_CAF1
Location 12,011,041 – 12,011,149
Length 108
Max. P 0.897010
window7528 window7529

overview

Window 8

Location 12,011,041 – 12,011,149
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.28
Mean single sequence MFE -44.83
Consensus MFE -32.06
Energy contribution -33.40
Covariance contribution 1.34
Combinations/Pair 1.11
Mean z-score -2.02
Structure conservation index 0.72
SVM decision value 1.00
SVM RNA-class probability 0.897010
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12011041 108 + 22224390
GGACUCGGCA------------GCAGCCGAUUCCUGAAUCUUAGUGGUACCAAAUCUACAGCAUUUAGUGAGGGCAACCAACGCCACAAUGGCCACCAGGCCAAUGGCCCAAAUCGAGGG
(((.(((((.------------...))))).)))....((((.((((........))))..........((((....))...((((...(((((....))))).)))).....)))))). ( -35.50)
>DroSec_CAF1 44569 120 + 1
GGCCUCGGCAUCAGCCUUUUUGGCAUCCGAGUCCUGAACCUUAGCGGUACCAGAUCCACACCAGAUGGUGAGGGCAACCAGCGCCACAAUGGCCAGCAGGCCAAUGGCCGGGCUCGAGGG
..((((.......(((.....)))....((((((.........((((........)).((((....)))).((....)).))((((...(((((....))))).)))).)))))))))). ( -49.50)
>DroSim_CAF1 43792 120 + 1
GGCCUCGGCAUUAUCCUUUUUGGCAUCCAAGUACUGAACCUUAUAGGUAUCAGAUCCACACCAGAUGGUGAGGGCAACCAGCGCCACAAUGGCCAGCAGGCCAAUGGCCGGGCCCGAGGG
((((.((((...........((((.........(((((((.....))).)))).....((((....)))).((....))...))))((.(((((....))))).))))))))))...... ( -49.50)
>consensus
GGCCUCGGCAU_A_CCUUUUUGGCAUCCGAGUCCUGAACCUUAGAGGUACCAGAUCCACACCAGAUGGUGAGGGCAACCAGCGCCACAAUGGCCAGCAGGCCAAUGGCCGGGCUCGAGGG
((.((((((...........((((.............(((.....)))..........((((....)))).((....))...))))((.(((((....))))).)))))))).))..... (-32.06 = -33.40 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,011,041 – 12,011,149
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.28
Mean single sequence MFE -47.23
Consensus MFE -33.35
Energy contribution -33.47
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.71
SVM decision value 0.54
SVM RNA-class probability 0.775459
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12011041 108 - 22224390
CCCUCGAUUUGGGCCAUUGGCCUGGUGGCCAUUGUGGCGUUGGUUGCCCUCACUAAAUGCUGUAGAUUUGGUACCACUAAGAUUCAGGAAUCGGCUGC------------UGCCGAGUCC
.......(((((((((((((((....)))))..)))))..((((.(((.((((........)).))...)))))))))))).....(((.(((((...------------.))))).))) ( -37.80)
>DroSec_CAF1 44569 120 - 1
CCCUCGAGCCCGGCCAUUGGCCUGCUGGCCAUUGUGGCGCUGGUUGCCCUCACCAUCUGGUGUGGAUCUGGUACCGCUAAGGUUCAGGACUCGGAUGCCAAAAAGGCUGAUGCCGAGGCC
.(((((.((.(((((..(((((....)))))...(((((((((((..((.((((....)))).))..((((.(((.....)))))))))).))).)))))....)))))..))))))).. ( -55.30)
>DroSim_CAF1 43792 120 - 1
CCCUCGGGCCCGGCCAUUGGCCUGCUGGCCAUUGUGGCGCUGGUUGCCCUCACCAUCUGGUGUGGAUCUGAUACCUAUAAGGUUCAGUACUUGGAUGCCAAAAAGGAUAAUGCCGAGGCC
......((((((((((.(((((....))))).))((((((..(.(((((.((((....)))).))...(((.(((.....))))))))).)..).)))))...........)))).)))) ( -48.60)
>consensus
CCCUCGAGCCCGGCCAUUGGCCUGCUGGCCAUUGUGGCGCUGGUUGCCCUCACCAUCUGGUGUGGAUCUGGUACCACUAAGGUUCAGGACUCGGAUGCCAAAAAGG_U_AUGCCGAGGCC
.(((.(((((..((((((((((....)))))..)))))...(((.(((((((((....)))).))....)))))).....)))))))).(((((..................)))))... (-33.35 = -33.47 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:37 2006