Locus 967

Sequence ID dm3.chr2L
Location 7,162,999 – 7,163,053
Length 54
Max. P 0.887550
window1318 window1319

overview

Window 8

Location 7,162,999 – 7,163,053
Length 54
Sequences 9
Columns 70
Reading direction forward
Mean pairwise identity 79.93
Shannon entropy 0.35868
G+C content 0.42708
Mean single sequence MFE -12.39
Consensus MFE -8.14
Energy contribution -8.53
Covariance contribution 0.40
Combinations/Pair 1.27
Mean z-score -1.48
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.607680
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7162999 54 + 23011544
--------CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG--------
--------(((.(..((((......))))..(((..(((((.....)))))...))).))))-------- ( -12.10, z-score =  -1.75, R)
>droPer1.super_8 866754 62 - 3966273
--------CUGACAUGGUUUCGCUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCGCACAGACAG
--------(((...(((((......))))).(((..(((((.....)))))...)))......))).... ( -14.00, z-score =  -1.43, R)
>dp4.chr4_group2 802102 62 + 1235136
--------CUGACAUGGUUUCGCUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCGCACAGACAG
--------(((...(((((......))))).(((..(((((.....)))))...)))......))).... ( -14.00, z-score =  -1.43, R)
>droAna3.scaffold_12943 1012005 61 - 5039921
CUGAAAACCUGGCAUGGUUUCG-UUAACCAGGCCAGAACGGAAAAUCUGUUAAAGGUAACGG--------
(((.....(((((.(((((...-..))))).)))))(((((.....)))))........)))-------- ( -19.10, z-score =  -2.76, R)
>droEre2.scaffold_4929 16078132 54 + 26641161
--------CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG--------
--------(((.(..((((......))))..(((..(((((.....)))))...))).))))-------- ( -12.10, z-score =  -1.75, R)
>droYak2.chr2L 16581811 54 - 22324452
--------CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG--------
--------(((.(..((((......))))..(((..(((((.....)))))...))).))))-------- ( -12.10, z-score =  -1.75, R)
>droSec1.super_3 2686624 54 + 7220098
--------CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG--------
--------(((.(..((((......))))..(((..(((((.....)))))...))).))))-------- ( -12.10, z-score =  -1.75, R)
>droSim1.chr2L 6952862 54 + 22036055
--------CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG--------
--------(((.(..((((......))))..(((..(((((.....)))))...))).))))-------- ( -12.10, z-score =  -1.75, R)
>droMoj3.scaffold_6500 27979399 54 - 32352404
--------CUGACAUGGUUUCGUUUAAGUGGCGCAGAGUGAAAAAAAAAAUACAAAUAUCAG--------
--------((((.((.((((..(((...(.((.....)).).)))..))))....)).))))-------- (  -3.90, z-score =   1.05, R)
>consensus
________CUGACACGGUUUCGUUUAACCAGGCCAAAACAGAAAAUCUGUUAAAGGUAGCAG________
........(((....((((......))))..(((..(((((.....)))))...)))..)))........ ( -8.14 =  -8.53 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,162,999 – 7,163,053
Length 54
Sequences 9
Columns 70
Reading direction reverse
Mean pairwise identity 79.93
Shannon entropy 0.35868
G+C content 0.42708
Mean single sequence MFE -11.88
Consensus MFE -9.75
Energy contribution -10.11
Covariance contribution 0.36
Combinations/Pair 1.27
Mean z-score -1.41
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.887550
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7162999 54 - 23011544
--------CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG--------
--------...........(((((.....))))).((((.(((((......))))).)))).-------- ( -12.00, z-score =  -1.68, R)
>droPer1.super_8 866754 62 + 3966273
CUGUCUGUGCGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAGCGAAACCAUGUCAG--------
..((((((............)))))).........((((.(((((......))))).)))).-------- ( -13.80, z-score =  -0.97, R)
>dp4.chr4_group2 802102 62 - 1235136
CUGUCUGUGCGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAGCGAAACCAUGUCAG--------
..((((((............)))))).........((((.(((((......))))).)))).-------- ( -13.80, z-score =  -0.97, R)
>droAna3.scaffold_12943 1012005 61 + 5039921
--------CCGUUACCUUUAACAGAUUUUCCGUUCUGGCCUGGUUAA-CGAAACCAUGCCAGGUUUUCAG
--------..((((....))))...........((((((.(((((..-...))))).))))))....... ( -16.00, z-score =  -2.55, R)
>droEre2.scaffold_4929 16078132 54 - 26641161
--------CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG--------
--------...........(((((.....))))).((((.(((((......))))).)))).-------- ( -12.00, z-score =  -1.68, R)
>droYak2.chr2L 16581811 54 + 22324452
--------CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG--------
--------...........(((((.....))))).((((.(((((......))))).)))).-------- ( -12.00, z-score =  -1.68, R)
>droSec1.super_3 2686624 54 - 7220098
--------CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG--------
--------...........(((((.....))))).((((.(((((......))))).)))).-------- ( -12.00, z-score =  -1.68, R)
>droSim1.chr2L 6952862 54 - 22036055
--------CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG--------
--------...........(((((.....))))).((((.(((((......))))).)))).-------- ( -12.00, z-score =  -1.68, R)
>droMoj3.scaffold_6500 27979399 54 + 32352404
--------CUGAUAUUUGUAUUUUUUUUUUCACUCUGCGCCACUUAAACGAAACCAUGUCAG--------
--------(((((((((((............................))))....)))))))-------- (  -3.29, z-score =   0.21, R)
>consensus
________CUGCUACCUUUAACAGAUUUUCUGUUUUGGCCUGGUUAAACGAAACCGUGUCAG________
...................(((((.....)))))(((((.(((((......))))).)))))........ ( -9.75 = -10.11 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:23:03 2011