Locus 4107

Sequence ID	X_DroMel_CAF1
Location	10,842,044 – 10,842,239
Length	195
Max. P	0.980762

overview

Window 9

Location	10,842,044 – 10,842,162
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.94
Mean single sequence MFE	-25.62
Consensus MFE	-24.64
Energy contribution	-24.45
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.46
Structure conservation index	0.96
SVM decision value	1.87
SVM RNA-class probability	0.980762
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10842044 118 + 22224390
CCUGCUUUUGGCCAACUAUUCCAAUUUCCCAUUCGCA--CCCCCGGUUGUACUGGAAUUUUUGGUCAUUACAAUCGUAAAUUAUUUUAUUUGCUGCUAAUUGCAGUUCACCAAAUGCCAA
.((((...(((((((..((((((..(..((.......--.....))..)...))))))..)))))))........((((((......))))))........))))............... ( -24.40)
>DroSec_CAF1 20847 118 + 1
GCUGCUUUUGACCAACUAUUCCAAUUUCCCAUUCGCA--CCCCCGGCUGUACUGGAAUUUUUGGUCAUUACAAUCGUAAAUUAUUUUAUUUGCUGCUAAUUGCAGUUCACCAAAUGCCAA
(((((...(((((((..((((((......((..((..--....))..))...))))))..)))))))........((((((......))))))........))))).............. ( -26.20)
>DroSim_CAF1 1709 118 + 1
CCUGCUUUUGGCCAACUAUUCCAAUUUCCCAUUCGCA--CCCCCGGCUGUACUGGAAUUUUUGGUCAUUACAAUCGUAAAUUAUUUUAUUUGCUGCUAAUUGCAGUUCACCAAAUGCCAA
.((((...(((((((..((((((......((..((..--....))..))...))))))..)))))))........((((((......))))))........))))............... ( -24.40)
>DroYak_CAF1 9834 120 + 1
GCUGCUUUUGGCCAACUAUUCCAAUAUCGCAUUCGCAGCCCCCCGUUUGUACUGGAAUUUUUGGUCAUUACAAUCGUAAAUUAUUUUAUUUGCUGCUAAUUGCAGUUCACUAAAUGCCAA
(((((...(((((((..((((((.....(((..((........))..)))..))))))..)))))))........((((((......))))))........))))).............. ( -27.50)
>consensus
CCUGCUUUUGGCCAACUAUUCCAAUUUCCCAUUCGCA__CCCCCGGCUGUACUGGAAUUUUUGGUCAUUACAAUCGUAAAUUAUUUUAUUUGCUGCUAAUUGCAGUUCACCAAAUGCCAA
........(((((((..((((((......((..((........))..))...))))))..)))))))((((....))))..(((((.....(((((.....))))).....))))).... (-24.64 = -24.45 +  -0.19)

alignment

secondary structure

dotplot

Window 0

Location	10,842,122 – 10,842,239
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-34.50
Consensus MFE	-19.48
Energy contribution	-21.98
Covariance contribution	2.50
Combinations/Pair	1.05
Mean z-score	-2.04
Structure conservation index	0.56
SVM decision value	0.02
SVM RNA-class probability	0.543747
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10842122 117 - 22224390
AGCCGCAGCGGCUGUGCGCCAAACACCAAGCCCGA---ACCCUCAUCCUUCGAUCCUUCGAGCUUGGUCGGUUGGUCAGUUUGGCAUUUGGUGAACUGCAAUUAGCAGCAAAUAAAAUAA
(((((...)))))...(((((((..((((((((.(---(((..(....(((((....)))))....)..))))))...))))))..)))))))..((((.....))))............ ( -36.60)
>DroSec_CAF1 20925 119 - 1
AGCCGCAGCGGCUGUGCGCCAAACACCAAGUCCGACUACCCCCCAUCCUUCGAUCC-UCGAGCUUGGUCGGUUGGUCAGUUUGGCAUUUGGUGAACUGCAAUUAGCAGCAAAUAAAAUAA
(((((...)))))...(((((((..(((((.(.(((((((..(((...((((....-.))))..)))..)).))))).))))))..)))))))..((((.....))))............ ( -39.50)
>DroSim_CAF1 1787 119 - 1
AGCCGCAGCGGCUGUGCGCCAAACACCAAGUCCGACUACCCCCCAUCCUUCGAUCC-UCGAGCUUGGUCGGUUGGUCAGUUUGGCAUUUGGUGAACUGCAAUUAGCAGCAAAUAAAAUAA
(((((...)))))...(((((((..(((((.(.(((((((..(((...((((....-.))))..)))..)).))))).))))))..)))))))..((((.....))))............ ( -39.50)
>DroYak_CAF1 9914 93 - 1
AGCCACAAC----------------CCAACGGCGA----CCCCCUUUCUCCGAUCC-UCGA------CCAACUGGUCAGUUUGGCAUUUAGUGAACUGCAAUUAGCAGCAAAUAAAAUAA
.((((.(((----------------....(((.((----.......)).)))....-..((------((....)))).)))))))((((.((...((((.....))))...)).)))).. ( -22.40)
>consensus
AGCCGCAGCGGCUGUGCGCCAAACACCAAGUCCGA___CCCCCCAUCCUUCGAUCC_UCGAGCUUGGUCGGUUGGUCAGUUUGGCAUUUGGUGAACUGCAAUUAGCAGCAAAUAAAAUAA
.((((.((((((.....)))....(((((..(((((((..........(((((....)))))..))))))))))))..)))))))((((.((...((((.....))))...)).)))).. (-19.48 = -21.98 +   2.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:31 2006