Locus 3080

Sequence ID dm3.chr2R
Location 2,066,068 – 2,066,119
Length 51
Max. P 0.893930
window4226 window4227

overview

Window 6

Location 2,066,068 – 2,066,119
Length 51
Sequences 7
Columns 55
Reading direction forward
Mean pairwise identity 78.82
Shannon entropy 0.43017
G+C content 0.39695
Mean single sequence MFE -8.17
Consensus MFE -8.10
Energy contribution -8.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.64
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.843918
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2066068 51 + 21146708
--AAAAUAAAAAAAUUC--GAAUACGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
--...............--......(((....(((((.......))))).))).. (  -8.10, z-score =  -0.90, R)
>droYak2.chr2L 1912626 53 - 22324452
--AAAACAAAAAAGUGUAAAAAUUCGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
--.......................(((....(((((.......))))).))).. (  -8.10, z-score =  -0.80, R)
>droEre2.scaffold_4929 6374984 51 - 26641161
--AAAACAAAAAAGUG--AAAGUCCGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
--..............--.......(((....(((((.......))))).))).. (  -8.10, z-score =  -0.38, R)
>droPer1.super_73 202093 50 - 267513
--CAAAUAAAAAAGAU---AUCUCCGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
--..............---......(((....(((((.......))))).))).. (  -8.10, z-score =  -0.55, R)
>droWil1.scaffold_180700 756544 54 - 6630534
AAUGUAA-AAAAAUUAUACAUCUGCGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
.(((((.-........)))))....(((....(((((.......))))).))).. (  -8.60, z-score =  -0.77, R)
>droVir3.scaffold_12875 4798489 52 + 20611582
---GUAAUGAAAAGAAAAAAUUAACGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
---......................(((....(((((.......))))).))).. (  -8.10, z-score =  -0.91, R)
>droMoj3.scaffold_6496 1594950 52 - 26866924
---AUAAUAAAAAGUUGAAUCUUGCGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
---......................(((....(((((.......))))).))).. (  -8.10, z-score =  -0.18, R)
>consensus
__AAAAAAAAAAAGUU_AAAAAUACGAUCCUGCCAGGAGUCGAACCUGGAAUCUU
.........................(((....(((((.......))))).))).. ( -8.10 =  -8.10 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 2,066,068 – 2,066,119
Length 51
Sequences 7
Columns 55
Reading direction reverse
Mean pairwise identity 78.82
Shannon entropy 0.43017
G+C content 0.39695
Mean single sequence MFE -10.89
Consensus MFE -9.40
Energy contribution -9.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.893930
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2066068 51 - 21146708
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGUAUUC--GAAUUUUUUUAUUUU--
..(((((((((.......)))))...))))......--...............-- (  -9.40, z-score =  -0.55, R)
>droYak2.chr2L 1912626 53 + 22324452
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGAAUUUUUACACUUUUUUGUUUU--
........((((((((.(((.....))))))))))).................-- (  -9.60, z-score =  -0.69, R)
>droEre2.scaffold_4929 6374984 51 + 26641161
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGGACUUU--CACUUUUUUGUUUU--
........((((((((.(((.....))))))))))).--..............-- ( -11.50, z-score =  -0.73, R)
>droPer1.super_73 202093 50 + 267513
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGGAGAU---AUCUUUUUUAUUUG--
..(((((((((.......)))))...))))((((..---..))))........-- (  -9.70, z-score =   0.10, R)
>droWil1.scaffold_180700 756544 54 + 6630534
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGCAGAUGUAUAAUUUUU-UUACAUU
..(((((((((.......)))))...))))...((((((........-.)))))) ( -11.90, z-score =  -1.61, R)
>droVir3.scaffold_12875 4798489 52 - 20611582
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGUUAAUUUUUUCUUUUCAUUAC---
..(((((((((.......)))))...))))......................--- (  -9.40, z-score =  -1.04, R)
>droMoj3.scaffold_6496 1594950 52 + 26866924
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGCAAGAUUCAACUUUUUAUUAU---
......(((((.......)))))..(((((....))))).............--- ( -14.70, z-score =  -2.88, R)
>consensus
AAGAUUCCAGGUUCGACUCCUGGCAGGAUCGCAAAUUU_AACUUUUUUUUUUU__
..(((((((((.......)))))...))))......................... ( -9.40 =  -9.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:16 2011