Locus 5320

Sequence ID	X_DroMel_CAF1
Location	13,906,677 – 13,906,818
Length	141
Max. P	0.782190

overview

Window 0

Location	13,906,677 – 13,906,783
Length	106
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	87.17
Mean single sequence MFE	-30.00
Consensus MFE	-22.46
Energy contribution	-21.15
Covariance contribution	-1.31
Combinations/Pair	1.23
Mean z-score	-1.86
Structure conservation index	0.75
SVM decision value	0.56
SVM RNA-class probability	0.782190
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13906677 106 + 22224390
UUUGUUUUCUUAUUUUGGCCUAGGUUUUCCCACUUUUCGAGCGACCGCCAAAAUGUUGCUGCAACAUGUUGCCGGCGAUCGCUUGUCCAAAGUUCUG---------ACAACUAAA
.(((((.....(((((((....((.....))......(((((((.((((...((((((...))))))......)))).))))))).)))))))...)---------))))..... ( -30.00)
>DroSim_CAF1 28895 114 + 1
UUUGUUUUCUUAUUUUGGCCUAGGCUUUU-CACUUUUCGAGCGACCGCCAAAAUGUUGCCGCAACAUGUUGCCGGCGAUCGCUUGUCCAAAGCUCUGAAAAAGUUGACAAAUAAA
((((((..(((.....(((....)))(((-((((((.(((((((.((((...((((((...))))))......)))).)))))))...))))...))))))))..)))))).... ( -33.20)
>DroEre_CAF1 2792 113 + 1
UUUAUUUUCUUUUUUUGGCCUAGGUUUUC-CACUUUUUGAGCGAAUGCCAAAAUGUUGCAGCAACAUGUUGCCGGCGAUCGCUUGUCCGAAACUCUGAA-AAGUUGACUAAUAAA
....(((((...((((((.(..((....)-).......((((((.((((........(((((.....))))).)))).))))))).))))))....)))-))............. ( -25.90)
>DroYak_CAF1 17214 114 + 1
UUUGUUUGCUUAUUUUGGUCUAGGUUUUCCCACUUUUUGAGCGGCCGCCAAAAUGUUGCGGCAACAUGUUGCCGGCGAUCGCUUGUCUGAAACUCUGAA-AAGUUGACAAAUAAA
((((((.((((.((..(((...((.....)).......(((((..((((((....))..(((((....)))))))))..))))).......)))..)).-)))).)))))).... ( -30.90)
>consensus
UUUGUUUUCUUAUUUUGGCCUAGGUUUUC_CACUUUUCGAGCGACCGCCAAAAUGUUGCAGCAACAUGUUGCCGGCGAUCGCUUGUCCAAAACUCUGAA_AAGUUGACAAAUAAA
............((((((...(((........)))..(((((((.((((...((((((...))))))......)))).))))))).))))))....................... (-22.46 = -21.15 +  -1.31)

alignment

secondary structure

dotplot

Window 1

Location	13,906,677 – 13,906,783
Length	106
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	87.17
Mean single sequence MFE	-29.17
Consensus MFE	-20.86
Energy contribution	-22.18
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-1.96
Structure conservation index	0.72
SVM decision value	0.56
SVM RNA-class probability	0.780696
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13906677 106 - 22224390
UUUAGUUGU---------CAGAACUUUGGACAAGCGAUCGCCGGCAACAUGUUGCAGCAACAUUUUGGCGGUCGCUCGAAAAGUGGGAAAACCUAGGCCAAAAUAAGAAAACAAA
....(((.(---------(.....(((((.(.(((((((((((....)((((((...))))))...)))))))))).).....((((....))))..)))))....)).)))... ( -32.20)
>DroSim_CAF1 28895 114 - 1
UUUAUUUGUCAACUUUUUCAGAGCUUUGGACAAGCGAUCGCCGGCAACAUGUUGCGGCAACAUUUUGGCGGUCGCUCGAAAAGUG-AAAAGCCUAGGCCAAAAUAAGAAAACAAA
(((((((.......(((((...(((((...(.(((((((((((((((....))))(....)....))))))))))).).))))))-))))((....))..)))))))........ ( -33.40)
>DroEre_CAF1 2792 113 - 1
UUUAUUAGUCAACUU-UUCAGAGUUUCGGACAAGCGAUCGCCGGCAACAUGUUGCUGCAACAUUUUGGCAUUCGCUCAAAAAGUG-GAAAACCUAGGCCAAAAAAAGAAAAUAAA
.(((((.((((((((-....)))))...)))......((((.(((((....)))))))....(((((((.((((((.....))))-))........)))))))...)).))))). ( -23.10)
>DroYak_CAF1 17214 114 - 1
UUUAUUUGUCAACUU-UUCAGAGUUUCAGACAAGCGAUCGCCGGCAACAUGUUGCCGCAACAUUUUGGCGGCCGCUCAAAAAGUGGGAAAACCUAGACCAAAAUAAGCAAACAAA
.....((((((((((-....)))))...)))))((((.(((((.(((.((((((...)))))).))).))).)).))......((((....))))...........))....... ( -28.00)
>consensus
UUUAUUUGUCAACUU_UUCAGAGCUUCGGACAAGCGAUCGCCGGCAACAUGUUGCAGCAACAUUUUGGCGGUCGCUCAAAAAGUG_GAAAACCUAGGCCAAAAUAAGAAAACAAA
........................(((((.(.(((((((((((....)((((((...))))))...))))))))))......((......))...).)))))............. (-20.86 = -22.18 +   1.31)

alignment

secondary structure

dotplot

Window 2

Location	13,906,712 – 13,906,818
Length	106
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	85.70
Mean single sequence MFE	-28.16
Consensus MFE	-19.55
Energy contribution	-20.59
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-1.77
Structure conservation index	0.69
SVM decision value	0.13
SVM RNA-class probability	0.597211
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13906712 106 - 22224390
GAAUCAAACAAUCUCUUUGUUUUUACUAUUAGUUUUUUAGUUGU---------CAGAACUUUGGACAAGCGAUCGCCGGCAACAUGUUGCAGCAACAUUUUGGCGGUCGCUCGAA
.............(((..(((((.((.(((((....))))).))---------.)))))...)))(.(((((((((((....)((((((...))))))...)))))))))).).. ( -30.60)
>DroSec_CAF1 7122 115 - 1
GAAUCAAACAAUCUCUUUGGUUUUACUAUUAGUUUUUUAUUUGUCAACUUUUUCAGAGCUUUGGGCAAGCGAUCGCCGGCAACAUGUUGCGGCAACAUUUUAGCGGUCGCUCGAA
((((((((.......))))))))..(((..((((((......(....)......)))))).))).(.(((((((((..((((....))))(....)......))))))))).).. ( -26.70)
>DroSim_CAF1 28929 115 - 1
GAAUCAAACAAUCUCUUUGUUUUUACUAUUGGUCUUUUAUUUGUCAACUUUUUCAGAGCUUUGGACAAGCGAUCGCCGGCAACAUGUUGCGGCAACAUUUUGGCGGUCGCUCGAA
.....((((((.....))))))......(((((((....((((..........)))).....)))).(((((((((((((((....))))(....)....)))))))))))))). ( -32.20)
>DroEre_CAF1 2826 114 - 1
GUCUCAAUCAAUCUAUUUGUUUUUACUAUUGAUUUUUUAUUAGUCAACUU-UUCAGAGUUUCGGACAAGCGAUCGCCGGCAACAUGUUGCUGCAACAUUUUGGCAUUCGCUCAAA
((((.((....(((....(((...((((.(((....))).)))).)))..-...)))..)).)))).(((((..((((....)((((((...))))))...)))..))))).... ( -24.40)
>DroYak_CAF1 17249 114 - 1
AGAUUAAUUAUUCUAUUUGUUUUUACCAUUGAUUUUUUAUUUGUCAACUU-UUCAGAGUUUCAGACAAGCGAUCGCCGGCAACAUGUUGCCGCAACAUUUUGGCGGCCGCUCAAA
(((........)))..............((((........((((((((((-....)))))...)))))(((...((((.(((.((((((...)))))).))).))))))))))). ( -26.90)
>consensus
GAAUCAAACAAUCUCUUUGUUUUUACUAUUGGUUUUUUAUUUGUCAACUU_UUCAGAGCUUUGGACAAGCGAUCGCCGGCAACAUGUUGCGGCAACAUUUUGGCGGUCGCUCGAA
........................................(((((..................)))))((((((((((....)((((((...))))))...)))))))))..... (-19.55 = -20.59 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:49 2006