Locus 101

Sequence ID	Bcere.0
Location	1,328,107 – 1,328,226
Length	119
Max. P	0.920523

overview

Window 4

Location	1,328,107 – 1,328,226
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.16
Mean single sequence MFE	-25.22
Consensus MFE	-12.99
Energy contribution	-16.30
Covariance contribution	3.31
Combinations/Pair	1.09
Mean z-score	-2.33
Structure conservation index	0.51
SVM decision value	0.52
SVM RNA-class probability	0.768334
Prediction	RNA

Download alignment: ClustalW | MAF

>Bcere.0 1328107 119 + 5224283/25-145
AAAGGGGUUGUCAUCUGACGUCGAAUCUUGUAAUAUAAUAAGCGUGAACGAAUUCACAUACAAACAUAUACCCCUUUGUUUGAACGUGAAAA-UUUCUCCCAUCCCCUUUAAUAUUUUUA
(((((((.((........(((((...(((((......)))))..)).)))..(((((...((((((..........))))))...)))))..-.......)).))))))).......... ( -25.20)
>Banth.0 1170777 119 + 5227293/25-145
AAAAGGGUUGUCAUCUGACGUCGAAUCUUGUAAUAUAAUAAGCGUGAACGAAUUCACAUACAAACAUAUACCCCUUUGUUUGAACGUGAAAA-UUUCUCCCAUCCCCUUUAAUAUUUUUA
.((((((..(((....)))...(((.(((((......)))))((....))..(((((...((((((..........))))))...)))))..-.))).......)))))).......... ( -21.40)
>Blich.0 1261459 120 + 4222334/25-145
AAAUCAGUUGUCAAAACUCGACAUGAUUUGAUAUUAUAAAGAUGUGAAAUUGAUCACAAACAAACAUUUACCCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUCGUUA
((((((((((........)))).))))))((((..(((((((((.((((((..((((...((((((..........))))))...))))..))))))...))))...))))))))).... ( -25.50)
>Bsubt.0 1232673 119 + 4214630/25-145
AUAGAGGUUGUCAAAAGUCGACAUCUUUUGUUAUCAUAAGGAUGUGAAAUUGAUCACAAACAAACAUU-ACCCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUCGUUA
(((((((....((((((.......)))))).........(((((.((((((..((((...((((((..-.......))))))...))))..))))))...))))))))))))........ ( -28.80)
>consensus
AAAGGGGUUGUCAAAAGACGACAAAUCUUGUAAUAAAAAAAACGUGAAAGAAAUCACAAACAAACAUAUACCCCUUUGUUUGAACGUGAAAA_UUUCUCCCAUCCCCUUUAAUAUCGUUA
(((((((.((................(((((......))))).(.((((((.(((((...((((((..........))))))...))))).)))))).).)).))))))).......... (-12.99 = -16.30 +   3.31)

alignment

secondary structure

dotplot

Window 5

Location	1,328,107 – 1,328,226
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.16
Mean single sequence MFE	-28.62
Consensus MFE	-20.98
Energy contribution	-22.60
Covariance contribution	1.62
Combinations/Pair	1.22
Mean z-score	-1.91
Structure conservation index	0.73
SVM decision value	1.13
SVM RNA-class probability	0.920523
Prediction	RNA

Download alignment: ClustalW | MAF

>Bcere.0 1328107 119 + 5224283/25-145
UAAAAAUAUUAAAGGGGAUGGGAGAAA-UUUUCACGUUCAAACAAAGGGGUAUAUGUUUGUAUGUGAAUUCGUUCACGCUUAUUAUAUUACAAGAUUCGACGUCAGAUGACAACCCCUUU
..........((((((((((((.(((.-..(((((((.((((((.(......).)))))).)))))))....)))...)))))..................(((....)))..))))))) ( -28.90)
>Banth.0 1170777 119 + 5227293/25-145
UAAAAAUAUUAAAGGGGAUGGGAGAAA-UUUUCACGUUCAAACAAAGGGGUAUAUGUUUGUAUGUGAAUUCGUUCACGCUUAUUAUAUUACAAGAUUCGACGUCAGAUGACAACCCUUUU
..........((((((((((((.(((.-..(((((((.((((((.(......).)))))).)))))))....)))...)))))).................(((....)))..)))))). ( -27.80)
>Blich.0 1261459 120 + 4222334/25-145
UAACGACAACAAAGGGGAUGGGAGAAAUUUUUCACGGUCAAACAAAGGGGUAAAUGUUUGUUUGUGAUCAAUUUCACAUCUUUAUAAUAUCAAAUCAUGUCGAGUUUUGACAACUGAUUU
.............(((((((...((((((..((((((.((((((..........)))))).))))))..)))))).)))))))........((((((((((((...))))))..)))))) ( -28.20)
>Bsubt.0 1232673 119 + 4214630/25-145
UAACGACAACAAAGGGGAUGGGAGAAAUUUUUCACGGUCAAACAAAGGGGU-AAUGUUUGUUUGUGAUCAAUUUCACAUCCUUAUGAUAACAAAAGAUGUCGACUUUUGACAACCUCUAU
...(((((.(...(((((((...((((((..((((((.((((((.......-..)))))).))))))..)))))).))))))).((....))...).))))).................. ( -29.60)
>consensus
UAAAAACAACAAAGGGGAUGGGAGAAA_UUUUCACGGUCAAACAAAGGGGUAAAUGUUUGUAUGUGAACAAGUUCACACCUAUAAUAUAACAAAAUACGACGACAGAUGACAACCCCUUU
..........((((((((((((.((((((.(((((((.((((((..........)))))).))))))).))))))...)))))...............(((((...)))))..))))))) (-20.98 = -22.60 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:24:57 2006