Locus 6278

Sequence ID	3R_DroMel_CAF1
Location	16,388,353 – 16,388,473
Length	120
Max. P	0.875040

overview

Window 7

Location	16,388,353 – 16,388,473
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.61
Mean single sequence MFE	-39.00
Consensus MFE	-26.31
Energy contribution	-27.12
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.70
Structure conservation index	0.67
SVM decision value	-0.02
SVM RNA-class probability	0.524198
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16388353 120 + 27905053
AUCCCAAUCGGGUUACUGAAUAAUGUUAUCCUUCUUCAGCUUGGCCAGCUCAUCCGGCCCGUAACCCAGUAGUUCGCCCAGCACUUCAUCCGUGUGCUGGCCAAGAAUCGGAGGAGCUGU
.......((((....)))).........((((((.....((((((((((......(((....(((......))).)))..((((.......))))))))))))))....))))))..... ( -37.30)
>DroSec_CAF1 9488 120 + 1
AUCCCAAUCGGUUUACUGAAUAAUGUUAUCCUUCUUCAGCUUGGCCAGCUCAUCCGGCCCGUAGCCCAGUAGUUGGCCCAACACUUUAUCCGUGUGCUGACCCAGAAUCGGAGGAGCUGU
.(((...((((....)))).........((((((((((((..((((((((.((..(((.....)))..))))))))))..((((.......)))))))))...))))..))))))..... ( -36.10)
>DroEre_CAF1 10034 120 + 1
CUCCAACUGGGGUUACUGGAUAAUGUUAUCCUUCUUAAGCUCGGCGAGCUCAUCCGGCCCGCACCCCAGUAGUUCACCCAGCACUUCAUCCGUGUGCUGGCCAAGAAUAGGAGGAGCUGU
((((.((((((((....(((((....)))))............(((.(((.....))).))))))))))).((((..(((((((.........)))))))....)))).))))....... ( -44.90)
>DroYak_CAF1 9635 117 + 1
UUGGAA---GGCUUACUGAAUAAUGUUAUCCUUCUUCAGCUUGGCCAGCUCAUCCGGCCCACAACCGAGUAGUUCACCCAGCACUUCAUCCGUGUGCUGGCCAAGAAUCGGAGGAGCUGU
..((((---((...((........))...)))))).((((((((((.........)))).....((((.........(((((((.........))))))).......))))..)))))). ( -37.69)
>consensus
AUCCAAAUCGGGUUACUGAAUAAUGUUAUCCUUCUUCAGCUUGGCCAGCUCAUCCGGCCCGCAACCCAGUAGUUCACCCAGCACUUCAUCCGUGUGCUGGCCAAGAAUCGGAGGAGCUGU
............................((((((.....((((((((((.(((..((.......)).(((.(((.....))))))......))).))))))))))....))))))..... (-26.31 = -27.12 +   0.81)

alignment

secondary structure

dotplot

Window 8

Location	16,388,353 – 16,388,473
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.61
Mean single sequence MFE	-43.38
Consensus MFE	-34.42
Energy contribution	-34.30
Covariance contribution	-0.12
Combinations/Pair	1.17
Mean z-score	-2.02
Structure conservation index	0.79
SVM decision value	0.89
SVM RNA-class probability	0.875040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16388353 120 - 27905053
ACAGCUCCUCCGAUUCUUGGCCAGCACACGGAUGAAGUGCUGGGCGAACUACUGGGUUACGGGCCGGAUGAGCUGGCCAAGCUGAAGAAGGAUAACAUUAUUCAGUAACCCGAUUGGGAU
........(((((((.(((.(((((((.........))))))).)))......(((((((.((((((.....))))))...........(((((....))))).)))))))))))))).. ( -46.00)
>DroSec_CAF1 9488 120 - 1
ACAGCUCCUCCGAUUCUGGGUCAGCACACGGAUAAAGUGUUGGGCCAACUACUGGGCUACGGGCCGGAUGAGCUGGCCAAGCUGAAGAAGGAUAACAUUAUUCAGUAAACCGAUUGGGAU
.((((((.(((.....(((.(((((((.........))))))).)))......((.(....).))))).)))))).((((((((((.((........)).)))))).......))))... ( -41.51)
>DroEre_CAF1 10034 120 - 1
ACAGCUCCUCCUAUUCUUGGCCAGCACACGGAUGAAGUGCUGGGUGAACUACUGGGGUGCGGGCCGGAUGAGCUCGCCGAGCUUAAGAAGGAUAACAUUAUCCAGUAACCCCAGUUGGAG
.......((((.....(((.(((((((.........))))))).)))...(((((((((((((((((.((....))))).)))).....(((((....))))).)).)))))))).)))) ( -45.70)
>DroYak_CAF1 9635 117 - 1
ACAGCUCCUCCGAUUCUUGGCCAGCACACGGAUGAAGUGCUGGGUGAACUACUCGGUUGUGGGCCGGAUGAGCUGGCCAAGCUGAAGAAGGAUAACAUUAUUCAGUAAGCC---UUCCAA
..(((((.((((....(((.(((((((.........))))))).))).((((......))))..)))).)))))(((...((((((.((........)).))))))..)))---...... ( -40.30)
>consensus
ACAGCUCCUCCGAUUCUUGGCCAGCACACGGAUGAAGUGCUGGGCGAACUACUGGGUUACGGGCCGGAUGAGCUGGCCAAGCUGAAGAAGGAUAACAUUAUUCAGUAACCCGAUUGGGAU
.((((((.(((.....(((.(((((((.........))))))).))).......(((.....)))))).)))))).....((((((.((........)).)))))).............. (-34.42 = -34.30 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:27 2006