Locus 6859

Sequence ID	dm3.chr3L
Location	10,301,862 – 10,301,964
Length	102
Max. P	0.800288

overview

Window 3

Location	10,301,862 – 10,301,964
Length	102
Sequences	7
Columns	109
Reading direction	forward
Mean pairwise identity	81.74
Shannon entropy	0.36322
G+C content	0.28768
Mean single sequence MFE	-22.75
Consensus MFE	-15.74
Energy contribution	-16.54
Covariance contribution	0.80
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.70
SVM RNA-class probability	0.790542
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 10301862 102 + 24543557
GCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA-------UUUUGUUUUUUUUUUGCACUCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((....(((((......)))))-------............(((((....)))))...))))))))))))..)))(((.....))).......... ( -24.10, z-score =  -1.89, R)
>droSim1.chr3L 9691527 100 + 22553184
GCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA---------UUUCUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((....(((((......)))))---------..........(((((....)))))...))))))))))))..)))(((.....))).......... ( -24.10, z-score =  -2.45, R)
>droSec1.super_0 2515792 104 + 21120651
GCUAAUUUGCAUAAAUUUUUGCAAAAA-ACCCGCAUUU----CUUUUUUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((....(((.....-....)))...----............(((((....)))))...))))))))))))..)))(((.....))).......... ( -19.30, z-score =   0.07, R)
>droYak2.chr3L 10290693 98 + 24197627
GCUAAUUUGCAUAAAUUUUUGCGAGUUUACUCGCU-----------UUUUUUUAUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((.....(((((....))))).-----------.......((((((....))))))..))))))))))))..)))(((.....))).......... ( -26.80, z-score =  -3.23, R)
>droEre2.scaffold_4784 10295042 108 + 25762168
GCUAAUUUGCAUAAAUUUU-GCGAAUUUACUCGCUAUUUUCUUUUUUUUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((....-((((......))))....................(((((....)))))...))))))))))))..)))(((.....))).......... ( -22.90, z-score =  -1.37, R)
>droAna3.scaffold_13337 15223213 96 + 23293914
GCUAAUUUGCAUAAAUUUUUGCAAUUUCGUUGGAG-------------UUUUUUGUUGGUUGUGCAAAUUUUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((..((((((...(((......-------------........)))...))))))...))))))))))))..)))(((.....))).......... ( -21.94, z-score =  -1.00, R)
>droVir3.scaffold_13049 16081072 87 + 25233164
GCUAAUUUGCAUAAAUUGUU----------UGGCAGUU----UUUUUUUUUUUUUUGGCAAA--------CCUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
((((((((((((((...(((----------((.(((..----............))).))))--------).)))))))))))..)))(((.....))).......... ( -20.14, z-score =  -1.25, R)
>consensus
GCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA________UUUUUUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUU
(((((((((((((((..((((((.......................................))))))...))))))))))))..)))(((.....))).......... (-15.74 = -16.54 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	10,301,862 – 10,301,964
Length	102
Sequences	7
Columns	109
Reading direction	reverse
Mean pairwise identity	81.74
Shannon entropy	0.36322
G+C content	0.28768
Mean single sequence MFE	-22.64
Consensus MFE	-16.01
Energy contribution	-17.66
Covariance contribution	1.65
Combinations/Pair	1.15
Mean z-score	-1.54
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.73
SVM RNA-class probability	0.800288
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 10301862 102 - 24543557
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGAGUGCAAAAAAAAAACAAAA-------UGCGAGUAAAUUCGCAAAAAUUUAUGCAAAUUAGC
....(((((((((.....((((((((.((((.......))))...))))))))..............-------((((((....))))))........))))))))).. ( -26.70, z-score =  -2.35, R)
>droSim1.chr3L 9691527 100 - 22553184
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAGAAA---------UGCGAGUAAAUUCGCAAAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((...(((((....)))))..........---------((((((....))))))....))))))))))))... ( -24.30, z-score =  -1.82, R)
>droSec1.super_0 2515792 104 - 21120651
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAAAAAAG----AAAUGCGGGU-UUUUUGCAAAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((...(((((((.((((..............----...)))).))-.....)))))..))))))))))))... ( -22.53, z-score =   0.20, R)
>droYak2.chr3L 10290693 98 - 24197627
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAUAAAAAAA-----------AGCGAGUAAACUCGCAAAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((..((((((....)))))).......-----------.(((((....))))).....))))))))))))... ( -27.60, z-score =  -3.39, R)
>droEre2.scaffold_4784 10295042 108 - 25762168
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAAAAAAAAGAAAAUAGCGAGUAAAUUCGC-AAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((...(((((....)))))....................(((((....)))))-....))))))))))))... ( -23.50, z-score =  -0.84, R)
>droAna3.scaffold_13337 15223213 96 - 23293914
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAAAAUUUGCACAACCAACAAAAAA-------------CUCCAACGAAAUUGCAAAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((...((((((..............-------------............))))))..))))))))))))... ( -17.07, z-score =  -1.64, R)
>droVir3.scaffold_13049 16081072 87 - 25233164
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAGG--------UUUGCCAAAAAAAAAAAAAA----AACUGCCA----------AACAAUUUAUGCAAAUUAGC
.........((((.....))))....(((((((((((.(--------((((.((.............----...)).))----------)))...)))))))))))... ( -16.79, z-score =  -0.91, R)
>consensus
AACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAAAAAA________UGCGAGUAAAUUCGCAAAAAUUUAUGCAAAUUAGC
.........((((.....))))....((((((((((((...(((((....)))))....................(((((....))))).....))))))))))))... (-16.01 = -17.66 +   1.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:15:47 2011