Locus 6658

Sequence ID	3R_DroMel_CAF1
Location	17,486,588 – 17,486,715
Length	127
Max. P	0.931597

overview

Window 3

Location	17,486,588 – 17,486,687
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	88.63
Mean single sequence MFE	-24.80
Consensus MFE	-16.82
Energy contribution	-17.50
Covariance contribution	0.68
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.68
SVM decision value	0.15
SVM RNA-class probability	0.606457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17486588 99 + 27905053
AAAUCAUCAUACUCGUGCACGCACGCACCCACACAAAUACAAGAACGGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACU
..............((((......))))..........((((.((..((..(((.(((((((((....))))))))).)))..))..)).))))..... ( -24.50)
>DroSec_CAF1 38812 97 + 1
AAAUCACCAUA-UCGUGCACGCACGCACCCACACAAAUACAACAACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUU-UUUGUUGUUUACU
...........-..((((......))))..........(((((((.(((..(((.(((((((((....))))))))).)))..))-))))))))..... ( -26.80)
>DroSim_CAF1 39836 98 + 1
AAAUCACCAUA-UCGUGCACGCACGCACCCACACAAAUACAACAACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACU
...........-..((((......))))..........(((((((.(((..(((.(((((((((....))))))))).)))..))).)))))))..... ( -28.00)
>DroEre_CAF1 39102 95 + 1
UAAUCCCGCUACUCUCGCACGCACACACCCACACAGCUACAC----AAGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACU
.......((.......))..............(((((.....----(((..(((.(((((((((....))))))))).)))..)))...)))))..... ( -19.90)
>DroYak_CAF1 40148 95 + 1
AAAUACCGCUACUCUCGCACGCACACACCCACACAACUACAA----AAGCCCAUAUGCUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACU
.......((.......))..............(((((...((----(((..(((.(((((((((....))))))))).)))..))))).)))))..... ( -24.80)
>consensus
AAAUCACCAUACUCGUGCACGCACGCACCCACACAAAUACAA_AACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACU
......................................((((.((.(((..(((.(((((((((....))))))))).)))..))).)).))))..... (-16.82 = -17.50 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	17,486,612 – 17,486,715
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	90.05
Mean single sequence MFE	-33.12
Consensus MFE	-26.14
Energy contribution	-27.22
Covariance contribution	1.08
Combinations/Pair	1.10
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	1.21
SVM RNA-class probability	0.931597
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17486612 103 + 27905053
GCACCCACACAAAUACAAGAACGGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACUUUCUGGGUUUUGACGGUGCGGUCAGCUG
(((((((.......((((.((..((..(((.(((((((((....))))))))).)))..))..)).))))........)))))..((((......)))))).. ( -31.76)
>DroSec_CAF1 38835 101 + 1
GCACCCACACAAAUACAACAACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUU-UUUGUUGUUUACUUUCUGGGU-UCGACGGCGCAGUCAGCUG
(((((((.......(((((((.(((..(((.(((((((((....))))))))).)))..))-))))))))........)))))-..(((......))).)).. ( -34.06)
>DroSim_CAF1 39859 102 + 1
GCACCCACACAAAUACAACAACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACUUUCUGGGC-UUGACGGCGCAGUCAGCUG
((.((((.......(((((((.(((..(((.(((((((((....))))))))).)))..))).)))))))........)))).-.((((......)))))).. ( -34.66)
>DroEre_CAF1 39126 99 + 1
ACACCCACACAGCUACAC----AAGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACUUUUUGGGUUUUGACGGCACGGUCAGCUG
.........(((((....----..(((((.....)))))(((..((((.((((((.......))))))(((.(((.....)))...)))))))..)))))))) ( -29.80)
>DroYak_CAF1 40172 99 + 1
ACACCCACACAACUACAA----AAGCCCAUAUGCUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACUUUUUGGGUUUUGACGGUGCCGUCAGCUG
..(((((...(((.((((----(((..(((.(((((((((....))))))))).)))...))))))).))).......))))).((((((....))))))... ( -35.30)
>consensus
GCACCCACACAAAUACAA_AACAGGCCCAUAUGUUGGGCGACGUUGCCCGGCAAAUGUUUUUUUUGUUGUUUACUUUCUGGGUUUUGACGGCGCAGUCAGCUG
..(((((.......((((.((.(((..(((.(((((((((....))))))))).)))..))).)).))))........))))).(((((......)))))... (-26.14 = -27.22 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:58 2006