Locus 7928

Sequence ID	dm3.chr3L
Location	18,641,964 – 18,642,094
Length	130
Max. P	0.743485

overview

Window 3

Location	18,641,964 – 18,642,065
Length	101
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	71.22
Shannon entropy	0.52615
G+C content	0.49531
Mean single sequence MFE	-31.62
Consensus MFE	-15.79
Energy contribution	-15.93
Covariance contribution	0.15
Combinations/Pair	1.42
Mean z-score	-1.30
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.35
SVM RNA-class probability	0.657202
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18641964 101 + 24543557
GAAGACUUGGGGGCAUGGGCAACCAUAUUGGAUGGCAAAAUGUGCCAGAAAGG---------AGCUUCGGCAGAAGCACACACACGGUUCCCUCUUCCGAUUUCGCUCUU--
(((((...((((((((((....))))......(((((.....)))))......---------.(((((....))))).........))))))))))).............-- ( -32.50, z-score =  -1.13, R)
>droAna3.scaffold_13337 4517411 109 - 23293914
---GAAGGGGAGGCAGUUCCAACUUUCUUCGAUAGCGUUUCGCAAAAAAUUCGCAAACAAGAAGCCACCAAGAAGGCACACACAUGCAUCCUUCGCAUGUUUUUUCUUAUUU
---((((((((((.(((....))).)))))....((((((.((.........)))))).....(((........)))........))..))))).................. ( -22.30, z-score =  -0.61, R)
>droEre2.scaffold_4784 10487140 100 - 25762168
GAAGGCUUGUGUGCAUGGGCAACCAUAUUGGGUGGCAAAAUGUGGGAG-AAGG---------AGCUUCGAAGGAAGCACACACACGGUUCCCUAUUCAGAUUUCGCUCUU--
....((......))((((....))))...((((((.((..((.(((((-..(.---------.(((((....))))).......)..)))))....))..))))))))..-- ( -28.60, z-score =  -0.29, R)
>droYak2.chr3L 8779876 109 - 24197627
GGAGACUUGUCUGCAUGGGCAACCGUAUUGGAUGGCAAAAUGUGGCAGAAAGGCAGA-AAGAAGCUUCGAAAGGAGCACAUACACGGUUCCCUACUCAGAUUUCCCUCUU--
((((....(((((..((((.((((((.(((.....)))..((((((......))...-.....(((((....))))).)))).)))))).))))..)))))....)))).-- ( -34.70, z-score =  -1.71, R)
>droSec1.super_19 622087 101 + 1257711
GAAGACUUGGUGGCAUGGGUAACCAUAUUGGAUGGCAAAGUGUGGCAGAAAGG---------AGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCUCCU--
........((.((.((((....))))((((((.(((((.(((((.(.....).---------.(((((....)))))...)))))..)))))...))))))...)).)).-- ( -34.30, z-score =  -1.49, R)
>droSim1.chr3L 17952261 101 + 22553184
GAAGACUUGGGGGCAUGGGUAACCAUAUUGGAUGGCAAAGUGUGGAAGGAAGG---------AGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCUCUU--
........(((((.((((....))))((((((.(((((.(((((........(---------.(((((....))))).).)))))..)))))...))))))..)))))..-- ( -37.30, z-score =  -2.58, R)
>consensus
GAAGACUUGGGGGCAUGGGCAACCAUAUUGGAUGGCAAAAUGUGGCAGAAAGG_________AGCUUCGAAAGAAGCACACACACGGUUCCCUAUUCCGAUUUCCCUCUU__
...........((.(((((.((((..........(((...)))....................(((((....)))))........)))).))))).)).............. (-15.79 = -15.93 +   0.15)

alignment

secondary structure

dotplot

Window 4

Location	18,642,000 – 18,642,094
Length	94
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	71.73
Shannon entropy	0.48935
G+C content	0.44993
Mean single sequence MFE	-25.54
Consensus MFE	-9.35
Energy contribution	-11.05
Covariance contribution	1.70
Combinations/Pair	1.40
Mean z-score	-2.22
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.56
SVM RNA-class probability	0.743485
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18642000 94 + 24543557
--------AAAAUGUGCCAGAAAGGAGCUUCGGCAGAAGCACACACACGGUUCCCUCUUCCGAUUUCGCUC--UUUAUCACUUUUUCUG-CCAUCUUCCGCAGAU----------
--------...........(((((((((.((((.((((((.(......))))...))).))))....))))--))).))......((((-(........))))).---------- ( -21.20, z-score =  -1.03, R)
>droAna3.scaffold_13337 4517448 112 - 23293914
---CGCAAAAAAUUCGCAAACAAGAAGCCACCAAGAAGGCACACACAUGCAUCCUUCGCAUGUUUUUUCUUAUUUUAUCCUGUUUUUGGUCCAAAGUCCAUAUGCUCCUUUUCGU
---.(((..........(((((.((.(((........)))....((((((.......))))))..............)).))))).(((.(....).)))..))).......... ( -19.00, z-score =  -0.88, R)
>droEre2.scaffold_4784 10487176 93 - 25762168
--------AAAAUGUGGGAG-AAGGAGCUUCGAAGGAAGCACACACACGGUUCCCUAUUCAGAUUUCGCUC--UUUAUCACUUUUUCUG-CCAUCUUCCACAGAU----------
--------....((((((((-(.((.(((((....)))))...................((((........--............))))-)).)))))))))...---------- ( -26.65, z-score =  -2.59, R)
>droYak2.chr3L 8779912 102 - 24197627
AAAAUGUGGCAGAAAGGCAGAAAGAAGCUUCGAAAGGAGCACAUACACGGUUCCCUACUCAGAUUUCCCUC--UUUAUCACUUUUUCUG-CCAUCUUCCACAGAU----------
....(((((.(((..((((((((((.(((((....)))))........((.((........))...))...--........))))))))-)).))).)))))...---------- ( -33.30, z-score =  -4.38, R)
>droSec1.super_19 622123 94 + 1257711
--------AAAGUGUGGCAGAAAGGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCUC--CUUAUCACUUUUUCUG-CCAUCUUCCACAGAU----------
--------.(((.((((((((((((.(((((....))))).......(((.........))).........--........))))))))-)))))))........---------- ( -25.80, z-score =  -2.20, R)
>droSim1.chr3L 17952297 94 + 22553184
--------AAAGUGUGGAAGGAAGGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCUC--UUUAUCACUUUUUCUG-CCAUCUUCCACAGAU----------
--------....((((((((((((...))))((((((((((.((.....))))).......(((.......--...))).....)))))-))..))))))))...---------- ( -27.30, z-score =  -2.25, R)
>consensus
________AAAAUGUGGCAGAAAGGAGCUUCGAAAGAAGCACACACACGGUUCCCUAUUCCGAUUUCCCUC__UUUAUCACUUUUUCUG_CCAUCUUCCACAGAU__________
............(((((.(((.(((((((((....))))).......(((.........)))......................)))).....))).)))))............. ( -9.35 = -11.05 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:36:10 2011