Locus 3295

Sequence ID	3R_DroMel_CAF1
Location	8,826,638 – 8,826,733
Length	95
Max. P	0.737137

overview

Window 1

Location	8,826,638 – 8,826,733
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	80.89
Mean single sequence MFE	-24.00
Consensus MFE	-16.29
Energy contribution	-16.82
Covariance contribution	0.53
Combinations/Pair	1.06
Mean z-score	-1.30
Structure conservation index	0.68
SVM decision value	-0.00
SVM RNA-class probability	0.532410
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8826638 95 + 27905053
GCUGGUGCACGAGGAUCUCUGCAAGAAGUGCAAUUCACUUCUCGAGCACCAUAACGAGUAAGUAGAUUGGGUAGAUUGUGCACCCAAUCUGAAAU
..((((((.((((((....((((.....))))......)))))).))))))...........((((((((((.(......))))))))))).... ( -33.10)
>DroVir_CAF1 1531 85 + 1
GCUGGUGCACGAGGACCUAUGCAAGAAGUGUAAUGCAAUGCUGGAACACCAUAAUGAGUGAGUGA------UUCA-UC--GAUAUAAC-UGCAGC
((((((.(....).)))...(((...(((((......))))).(((((((((.....))).))).------))).-..--........-)))))) ( -14.90)
>DroSec_CAF1 1105 87 + 1
GCUGGUGCACGAGGAUCUCUGCAAGAAGUGCAAUUCACUUCUCGAGCACCAUAACGAGUAAGUUG------CACAAUC--UACGCAACCUGAAAU
..((((((.((((((....((((.....))))......)))))).))))))..........((((------(......--...)))))....... ( -24.70)
>DroSim_CAF1 1062 87 + 1
GCUGGUGCACGAGGAUCUCUGCAAGAAGUGCAAUUCACUUCUCGAGCACCAUAACGAGUAAGUUG------CACAAUC--UGCGCAACCUGAAAU
..((((((.((((((....((((.....))))......)))))).))))))..........((((------(.(....--.).)))))....... ( -26.20)
>DroEre_CAF1 1130 87 + 1
GCUGGUGCACGAGGAUCUCUGCAAGAAAUGCAAUUCUCUUCUCGAGCACCAUAACGAGUAGGUUU------CACGAGC--CUCGCGACCUGAAAU
..((((((.((((((....((((.....))))......)))))).))))))...((.(.((((((------...))))--))).))......... ( -26.30)
>DroYak_CAF1 1048 87 + 1
GCUUGUGCACGAGGAUCUCUGCAAGAAGUGCAAUUCUCUUCUCGAGCACCAUAACGAGUAAGUUU------UACGAGC--CACGUGACCUGAAAU
((((((((.((((((....((((.....))))......)))))).))))........(((.....------)))))))--............... ( -18.80)
>consensus
GCUGGUGCACGAGGAUCUCUGCAAGAAGUGCAAUUCACUUCUCGAGCACCAUAACGAGUAAGUUG______CACAAUC__CACGCAACCUGAAAU
..((((((.((((((....((((.....))))......)))))).))))))............................................ (-16.29 = -16.82 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	8,826,638 – 8,826,733
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	80.89
Mean single sequence MFE	-27.37
Consensus MFE	-15.79
Energy contribution	-16.32
Covariance contribution	0.53
Combinations/Pair	1.07
Mean z-score	-2.19
Structure conservation index	0.58
SVM decision value	0.44
SVM RNA-class probability	0.737137
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8826638 95 - 27905053
AUUUCAGAUUGGGUGCACAAUCUACCCAAUCUACUUACUCGUUAUGGUGCUCGAGAAGUGAAUUGCACUUCUUGCAGAGAUCCUCGUGCACCAGC
.....((((((((((.......))))))))))............((((((.(((((((((.....)))))))))..(((...)))..)))))).. ( -34.90)
>DroVir_CAF1 1531 85 - 1
GCUGCA-GUUAUAUC--GA-UGAA------UCACUCACUCAUUAUGGUGUUCCAGCAUUGCAUUACACUUCUUGCAUAGGUCCUCGUGCACCAGC
...((.-........--((-(((.------........))))).((((((....((..((((..........))))...))......)))))))) ( -14.30)
>DroSec_CAF1 1105 87 - 1
AUUUCAGGUUGCGUA--GAUUGUG------CAACUUACUCGUUAUGGUGCUCGAGAAGUGAAUUGCACUUCUUGCAGAGAUCCUCGUGCACCAGC
.....((((((((..--.....))------))))))........((((((.(((((((((.....)))))))))..(((...)))..)))))).. ( -29.40)
>DroSim_CAF1 1062 87 - 1
AUUUCAGGUUGCGCA--GAUUGUG------CAACUUACUCGUUAUGGUGCUCGAGAAGUGAAUUGCACUUCUUGCAGAGAUCCUCGUGCACCAGC
.....(((((((((.--....)))------))))))........((((((.(((((((((.....)))))))))..(((...)))..)))))).. ( -33.60)
>DroEre_CAF1 1130 87 - 1
AUUUCAGGUCGCGAG--GCUCGUG------AAACCUACUCGUUAUGGUGCUCGAGAAGAGAAUUGCAUUUCUUGCAGAGAUCCUCGUGCACCAGC
.(((((((((....)--)))..))------)))...........((((((.((((..((...(((((.....)))))...)))))).)))))).. ( -29.90)
>DroYak_CAF1 1048 87 - 1
AUUUCAGGUCACGUG--GCUCGUA------AAACUUACUCGUUAUGGUGCUCGAGAAGAGAAUUGCACUUCUUGCAGAGAUCCUCGUGCACAAGC
...........((((--((..(((------.....)))..))))))((((.((((..((...(((((.....)))))...)))))).)))).... ( -22.10)
>consensus
AUUUCAGGUUGCGUG__GAUUGUA______CAACUUACUCGUUAUGGUGCUCGAGAAGUGAAUUGCACUUCUUGCAGAGAUCCUCGUGCACCAGC
............................................((((((.((((.......(((((.....))))).....)))).)))))).. (-15.79 = -16.32 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:50 2006