Locus 6976

Sequence ID 3L_DroMel_CAF1
Location 18,824,610 – 18,824,745
Length 135
Max. P 0.892645
window11314 window11315

overview

Window 4

Location 18,824,610 – 18,824,712
Length 102
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 97.41
Mean single sequence MFE -35.80
Consensus MFE -33.50
Energy contribution -33.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.94
SVM decision value 0.97
SVM RNA-class probability 0.892645
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18824610 102 - 23771897
GGCCGGGAAGGCAGCGAAAGGGCCA-AACGAAUGCAAGUGGGCGCCACUUAAGCCGAAAGGAAAAGGUAGAGCAAGUGCUAAUCAUUGCUAGAUGCCUGCCAC
(((((....(((..(....).))).-..)).....((((((...))))))..)))....((...(((((.(((((..........)))))...))))).)).. ( -32.00)
>DroSec_CAF1 31996 103 - 1
GGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUCGGCCGACAGGAAAAGGUAGAGCAAGUGCUAAUCAUUGCUAGAUGCCUGCCAC
(((((((..(((..(....).(((...((........)).))))))..)))))))....((...(((((.(((((..........)))))...))))).)).. ( -39.50)
>DroSim_CAF1 33133 103 - 1
GGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUAGGCCGACAGGAAAAGGUAGAGCAAGUGCUAAUCAUUGCUAGAUGCCUGCCAC
((((.....(((..(....).)))...........((((((...)))))).))))....((...(((((.(((((..........)))))...))))).)).. ( -35.90)
>consensus
GGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUAGGCCGACAGGAAAAGGUAGAGCAAGUGCUAAUCAUUGCUAGAUGCCUGCCAC
((((.....(((..(....).(((...((........)).)))))).....))))....((...(((((.(((((..........)))))...))))).)).. (-33.50 = -33.83 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,824,639 – 18,824,745
Length 106
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 97.51
Mean single sequence MFE -33.27
Consensus MFE -30.90
Energy contribution -31.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.93
SVM decision value 0.86
SVM RNA-class probability 0.867631
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18824639 106 - 23771897
CAACAUUUCAAUAUGCUAAUUACUUUUCGACUUGGCCGGGAAGGCAGCGAAAGGGCCA-AACGAAUGCAAGUGGGCGCCACUUAAGCCGAAAGGAAAAGGUAGAGCA
.............((((.....(((((((.....(((.....)))..)))))))(((.-.........((((((...))))))...((....))....)))..)))) ( -29.60)
>DroSec_CAF1 32025 107 - 1
CAACAUUUCAAUAUGCUAAUUACUUUUCGACUUGGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUCGGCCGACAGGAAAAGGUAGAGCA
.............((((.....((((((...(((((((((..(((..(....).(((...((........)).))))))..)))))))))...))))))....)))) ( -36.90)
>DroSim_CAF1 33162 107 - 1
CAACAUUUCAAUAUGCUAAUUACUUUUCGACUUGGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUAGGCCGACAGGAAAAGGUAGAGCA
.............((((.....((((((...((((((.....(((..(....).)))...........((((((...)))))).))))))...))))))....)))) ( -33.30)
>consensus
CAACAUUUCAAUAUGCUAAUUACUUUUCGACUUGGCCGGGAAGGCAGCGAAAGGGCCAAAACGAAUGCAAGUGGGCGCCACUUAGGCCGACAGGAAAAGGUAGAGCA
.............((((.....((((((...((((((.....(((..(....).(((...((........)).)))))).....))))))...))))))....)))) (-30.90 = -31.23 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:35 2006