Locus 8331

Sequence ID dm3.chr3L
Location 22,064,942 – 22,065,064
Length 122
Max. P 0.777040
window11443 window11444

overview

Window 3

Location 22,064,942 – 22,065,064
Length 122
Sequences 5
Columns 125
Reading direction forward
Mean pairwise identity 73.07
Shannon entropy 0.46922
G+C content 0.49014
Mean single sequence MFE -35.70
Consensus MFE -21.20
Energy contribution -21.45
Covariance contribution 0.25
Combinations/Pair 1.21
Mean z-score -1.09
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.530212
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22064942 122 + 24543557
GUCUGUGCGGAGGCUAUCGAUGGAGGAGGCUAUG-GUCACGCGUCAUCGAUAAGCAGCAGUGCUGGCGGCCAGCUUUUUUCAAGCCAAGCUAUUGCUUCGGAAUAAA-AUCGCUAAGUUUUUGG-
(((.(..(.(..((((((((((..((.(((....-))).).)..))))))).)))..).)..).)))....(((..((((....((((((....)))).))...)))-)..)))..........- ( -35.40, z-score =   0.78, R)
>droEre2.scaffold_4784 21741307 98 + 25762168
----------GGCUUAUCGAUGGCG----------------CGUCAUCGAUAGACAGCAGUGUUGCCGGCCAGCCGUUUUCAAGCCAAAAAAUUUUUUUUGGCAAAAUAAAGCUAAAUUCUAUA-
----------.(..(((((((((..----------------..)))))))))..)(((..((((..(((....))).......((((((((....))))))))..))))..)))..........- ( -28.30, z-score =  -2.12, R)
>droYak2.chr3L_random 217157 95 + 4797643
GUCUGAGCGGAGGCUAUCGAUUGCG----CUAU--------CGUCAUCGAUAGGCAGCAGUGCUGACGGCCAGCCGUUUUCAAGCCAAG----------------AA-AUCGCUAAAUUUUUGG-
.....(((((.(.((((((((.(((----....--------))).)))))))).).((..((..(((((....)))))..)).))....----------------..-.)))))..........- ( -29.90, z-score =  -0.68, R)
>droSec1.super_11 1999721 120 + 2888827
GUCUGUGCGGAGGCUAUCGAUGGCG----CUAUCAGUCACGCGUCAUCGAUAGGCAGCUGUGUUGGCGGCCAGCUUUUUUCAAGCCAGGCAAUUGCUUCGGUAUAAA-AUCGCUAAAUUUUUGGA
......((((..(((((((((((((----(..........)))))))))))).))..)))).(((((((((.((((.....))))..)))...(((....)))....-..))))))......... ( -43.60, z-score =  -2.18, R)
>droSim1.chr3L 21411377 120 + 22553184
GUCUGUGCGGAGGCUAUCGAUGGCG----CUAUCAGUCACGCGUCAUCGAUAGGCAGCUGUGUUGGCGGCCAGCUUUUUUCAAGCCAGGCAAUUGCUUCGGGAUAAA-AUCGCUAAAUUUUUGGA
......((((..(((((((((((((----(..........)))))))))))).))..)))).(((((((((.((((.....))))..))).....(....)......-..))))))......... ( -41.30, z-score =  -1.22, R)
>consensus
GUCUGUGCGGAGGCUAUCGAUGGCG____CUAU__GUCACGCGUCAUCGAUAGGCAGCAGUGUUGGCGGCCAGCUUUUUUCAAGCCAAGCAAUUGCUUCGGGAUAAA_AUCGCUAAAUUUUUGG_
...........(.((((((((((((................)))))))))))).)(((...((((.....))))............((((....)))).............)))........... (-21.20 = -21.45 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 22,064,942 – 22,065,064
Length 122
Sequences 5
Columns 125
Reading direction reverse
Mean pairwise identity 73.07
Shannon entropy 0.46922
G+C content 0.49014
Mean single sequence MFE -29.96
Consensus MFE -16.31
Energy contribution -16.71
Covariance contribution 0.40
Combinations/Pair 1.14
Mean z-score -1.57
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.777040
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22064942 122 - 24543557
-CCAAAAACUUAGCGAU-UUUAUUCCGAAGCAAUAGCUUGGCUUGAAAAAAGCUGGCCGCCAGCACUGCUGCUUAUCGAUGACGCGUGAC-CAUAGCCUCCUCCAUCGAUAGCCUCCGCACAGAC
-...........(((.(-((((..((.((((....))))))..)))))...(((((...)))))......(((.(((((((..((.....-....))......))))))))))...)))...... ( -29.20, z-score =  -0.57, R)
>droEre2.scaffold_4784 21741307 98 - 25762168
-UAUAGAAUUUAGCUUUAUUUUGCCAAAAAAAAUUUUUUGGCUUGAAAACGGCUGGCCGGCAACACUGCUGUCUAUCGAUGACG----------------CGCCAUCGAUAAGCC----------
-..........((((((.((..((((((((....))))))))..)).)).))))((((((((....)))))..((((((((...----------------...)))))))).)))---------- ( -29.30, z-score =  -2.86, R)
>droYak2.chr3L_random 217157 95 - 4797643
-CCAAAAAUUUAGCGAU-UU----------------CUUGGCUUGAAAACGGCUGGCCGUCAGCACUGCUGCCUAUCGAUGACG--------AUAG----CGCAAUCGAUAGCCUCCGCUCAGAC
-(((((((((....)))-))----------------.)))).((((...(((..(((..(((((...)))((((((((....))--------))))----.))....))..))).))).)))).. ( -25.50, z-score =  -0.56, R)
>droSec1.super_11 1999721 120 - 2888827
UCCAAAAAUUUAGCGAU-UUUAUACCGAAGCAAUUGCCUGGCUUGAAAAAAGCUGGCCGCCAACACAGCUGCCUAUCGAUGACGCGUGACUGAUAG----CGCCAUCGAUAGCCUCCGCACAGAC
............(((..-...........(((...(((.(((((.....)))))))).((.......)))))(((((((((.(((..........)----)).)))))))))....)))...... ( -32.90, z-score =  -2.01, R)
>droSim1.chr3L 21411377 120 - 22553184
UCCAAAAAUUUAGCGAU-UUUAUCCCGAAGCAAUUGCCUGGCUUGAAAAAAGCUGGCCGCCAACACAGCUGCCUAUCGAUGACGCGUGACUGAUAG----CGCCAUCGAUAGCCUCCGCACAGAC
............(((..-...........(((...(((.(((((.....)))))))).((.......)))))(((((((((.(((..........)----)).)))))))))....)))...... ( -32.90, z-score =  -1.85, R)
>consensus
_CCAAAAAUUUAGCGAU_UUUAUCCCGAAGCAAUUGCUUGGCUUGAAAAAAGCUGGCCGCCAACACUGCUGCCUAUCGAUGACGCGUGAC__AUAG____CGCCAUCGAUAGCCUCCGCACAGAC
..........((((.......................(..((((.....))))..)..(....)...)))).(((((((((.((................)).)))))))))............. (-16.31 = -16.71 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:38 2011