Locus 5892

Sequence ID dm3.chr3L
Location 2,192,030 – 2,192,122
Length 92
Max. P 0.579415
window8101 window8102

overview

Window 1

Location 2,192,030 – 2,192,122
Length 92
Sequences 8
Columns 93
Reading direction forward
Mean pairwise identity 76.43
Shannon entropy 0.46795
G+C content 0.33016
Mean single sequence MFE -18.75
Consensus MFE -7.04
Energy contribution -7.16
Covariance contribution 0.13
Combinations/Pair 1.38
Mean z-score -2.08
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.579415
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 2192030 92 + 24543557
AACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAGGUGUUGU-GGGAAACUUUUCUAUUUUUAUACUGCACUAACUAAAUUAGUU
(((((((((((((((.....))))))))).........(((..(((..((-((((.....))))))...)))..)))..........)))))) ( -25.10, z-score =  -3.59, R)
>droSim1.chr3L 1748334 91 + 22553184
AACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGUUUG-GG-AAACUUUUCUAUUUUUAUACUAUACUAACUAAAUUAGUU
(((((((((((((((.....))))))))((((((((.....))))))))(-(.-...))...........................))))))) ( -21.10, z-score =  -3.38, R)
>droSec1.super_2 2218067 92 + 7591821
AACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGUUUG-GGGAAACUUUUCUAUUUUUAUACUAUACUAACUAAAUUAGUU
(((((((((((((((.....))))))))((((((((.....))))))))(-((....)))..........................))))))) ( -21.60, z-score =  -3.17, R)
>droEre2.scaffold_4784 2186716 92 + 25762168
AACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUAAGCAAUGUGUUUG-GGAAAACUUUUCUAUUUUUAUAAUAUAAUAACUAAAUUAGUU
((((((((((((((((...)))))))))((((((((.....))))))))(-((((....)))))......................))))))) ( -21.10, z-score =  -2.92, R)
>droYak2.chr3L 2145361 92 + 24197627
AACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUACGUAAUGUGUUUG-GGAAAACUUUUCUAUUUUUAUAAUAUAAUUACUAAAUUAGUU
((((((((((((((((...)))))))))).........((((((((((..-.(((((........)))))..))))).)))))....)))))) ( -23.40, z-score =  -3.44, R)
>droAna3.scaffold_13337 22649100 92 - 23293914
CUCUGAAUCCGACACACGC-GUGUCUAAACCCACAGAAACGGGGUGGGGGCGUAAAACUUUUCUAUUUUUGUUCUAAAUUAGCUAAAUUAAUA
..((((..(((((((....-)))))...((((.(......)))))))(((((.((((........)))))))))....))))........... ( -15.70, z-score =   0.51, R)
>dp4.chrXR_group6 12103238 74 + 13314419
AACUAAAUCCGACACACGC-GUGUCAU--------UAAGCAGUG-------GGAAAAGUUGUCUAUUUUUAU---GUAAUAAAUAAAUUAACA
..........(((((....-)))))((--------((....(((-------((((.((....)).)))))))---.))))............. ( -10.00, z-score =  -0.02, R)
>droPer1.super_33 126212 74 + 967471
AACUAAAUCCGACACACGC-GUGUCAU--------UAAGCAGUG-------GGAAAAGUUGUCUAUUUUUAU---GCAAUAACUAAAUUAACA
..........(((((....-)))))..--------...(((.((-------((((.((....)).)))))))---))................ ( -12.00, z-score =  -0.65, R)
>consensus
AACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUAAGCAAUGUGUUUG_GGAAAACUUUUCUAUUUUUAUACUAUAAUAACUAAAUUAGUU
.......((((((((.....)))))....(((((.........)))))...)))....................................... ( -7.04 =  -7.16 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,192,030 – 2,192,122
Length 92
Sequences 8
Columns 93
Reading direction reverse
Mean pairwise identity 76.43
Shannon entropy 0.46795
G+C content 0.33016
Mean single sequence MFE -15.51
Consensus MFE -9.62
Energy contribution -10.01
Covariance contribution 0.39
Combinations/Pair 1.25
Mean z-score -0.98
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.521816
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 2192030 92 - 24543557
AACUAAUUUAGUUAGUGCAGUAUAAAAAUAGAAAAGUUUCCC-ACAACACCUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUU
((((((..........((((..........(((....)))..-........)))).........(((((((((.....))))))))))))))) ( -18.25, z-score =  -1.16, R)
>droSim1.chr3L 1748334 91 - 22553184
AACUAAUUUAGUUAGUAUAGUAUAAAAAUAGAAAAGUUU-CC-CAAACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUU
((((((........((((((((........(((....))-).-.........))).)))))...(((((((((.....))))))))))))))) ( -17.67, z-score =  -1.59, R)
>droSec1.super_2 2218067 92 - 7591821
AACUAAUUUAGUUAGUAUAGUAUAAAAAUAGAAAAGUUUCCC-CAAACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUU
((((((........((((((((....................-.........))).)))))...(((((((((.....))))))))))))))) ( -17.25, z-score =  -1.43, R)
>droEre2.scaffold_4784 2186716 92 - 25762168
AACUAAUUUAGUUAUUAUAUUAUAAAAAUAGAAAAGUUUUCC-CAAACACAUUGCUUAUAUAUUUUCCGACACGGCGCGUGUCGGAAUUAGUU
((((((((................((((((...((((.....-..........))))...))))))((((((((...)))))))))))))))) ( -18.86, z-score =  -2.52, R)
>droYak2.chr3L 2145361 92 - 24197627
AACUAAUUUAGUAAUUAUAUUAUAAAAAUAGAAAAGUUUUCC-CAAACACAUUACGUAUAUAUUUUCCGACACGGCGCGUGUCGGAAUUAGUU
((((((....(((((.........(((((......)))))..-.......))))).........((((((((((...)))))))))))))))) ( -19.67, z-score =  -2.74, R)
>droAna3.scaffold_13337 22649100 92 + 23293914
UAUUAAUUUAGCUAAUUUAGAACAAAAAUAGAAAAGUUUUACGCCCCCACCCCGUUUCUGUGGGUUUAGACAC-GCGUGUGUCGGAUUCAGAG
....(((((..(((.(((......))).)))..))))).....(((((((.........)))))....(((((-....)))))))........ ( -15.10, z-score =   0.25, R)
>dp4.chrXR_group6 12103238 74 - 13314419
UGUUAAUUUAUUUAUUAC---AUAAAAAUAGACAACUUUUCC-------CACUGCUUA--------AUGACAC-GCGUGUGUCGGAUUUAGUU
((((.((((.........---....)))).))))........-------.((((....--------.((((((-....))))))....)))). (  -8.62, z-score =   0.34, R)
>droPer1.super_33 126212 74 - 967471
UGUUAAUUUAGUUAUUGC---AUAAAAAUAGACAACUUUUCC-------CACUGCUUA--------AUGACAC-GCGUGUGUCGGAUUUAGUU
((((.((((.........---....)))).))))........-------.((((....--------.((((((-....))))))....)))). (  -8.62, z-score =   1.04, R)
>consensus
AACUAAUUUAGUUAUUAUAGUAUAAAAAUAGAAAAGUUUUCC_CAAACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUU
.................................................................((((((((.....))))))))....... ( -9.62 = -10.01 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:57:12 2011