Locus 8232

Sequence ID	dm3.chr3L
Location	21,193,811 – 21,193,924
Length	113
Max. P	0.833325

overview

Window 3

Location	21,193,811 – 21,193,924
Length	113
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	88.20
Shannon entropy	0.20078
G+C content	0.60955
Mean single sequence MFE	-42.74
Consensus MFE	-33.22
Energy contribution	-33.18
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.78
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.00
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>dm3.chr3L 21193811 113 + 24543557
GCAUGGGUAUGGUGGUAUGGGUUAUGGGUUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGC--
..........((((((.(((((.(((.(((((((((((((.....(((.((((....)))).))).....))))..))))..)))))..)))...))))).....))))))..-- ( -43.70, z-score =  -0.94, R)
>droEre2.scaffold_4784 20878527 98 + 25762168
GCACGGG--------UAUGG--------CUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGCA-
((.(((.--------..((.--------((.(((((((((.(..((((.((((....)))).))(((..((...))..)))....))..).))))))))).)).)))))..)).- ( -39.20, z-score =  -0.97, R)
>droYak2.chr3L 4865623 104 - 24197627
GCACGGGAUUG---UUAUGG--------UUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUCAGUGACAACAUUUCGCCCAGAGCCGCCGCCGCAG
((.(((.....---...(((--------((.(((((((((.(..((((.((((....)))).))(((..((...))..)))....))..).))))))))).))))))))..)).. ( -39.90, z-score =  -1.61, R)
>droSec1.super_11 1147325 106 + 2888827
GCAUGGGUAUGGUGGUAUGG--------UUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUUGGUGACAACAUUUCGCCCAGAGGCGUCGCCGCG-
...........((((((((.--------((.(((((((((.(..(((((((((....)))).((..((....))..))...))).))..).))))))))).)).))).))))).- ( -42.20, z-score =  -1.28, R)
>droSim1.chr3L 20551739 106 + 22553184
GCAUGGGUAUGGCGGUAUGG--------UUAUGGGUGAAGUGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUUGGUGACAACAUUUCGCCCAGAGGCGUCGCCGCG-
...........((((((((.--------((.(((((((((((..(((((((((....)))).((..((....))..))...))).))..))))))))))).)).))).))))).- ( -48.70, z-score =  -3.17, R)
>consensus
GCAUGGGUAUGG_GGUAUGG________UUAUGGGUGAAGCGACGUGCCGGGCGAAAGCCCAGCGAGAAUCUUCGAGCCUCAGUGACAACAUUUCGCCCAGAGGCGCCGCCGCA_
((.............................(((((((((.(..((((.((((....)))).))(((..((...))..)))....))..).)))))))))..(((...))))).. (-33.22 = -33.18 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	21,193,811 – 21,193,924
Length	113
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	88.20
Shannon entropy	0.20078
G+C content	0.60955
Mean single sequence MFE	-37.24
Consensus MFE	-34.04
Energy contribution	-34.84
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.91
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.84
SVM RNA-class probability	0.833325
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21193811 113 - 24543557
--GCGGCGGCGCCUCUGGGCGAAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAACCCAUAACCCAUACCACCAUACCCAUGC
--(((((((.(((((..(((((....)))))...))))).)..........(((((((....))))))).))))))....................................... ( -39.10, z-score =  -1.93, R)
>droEre2.scaffold_4784 20878527 98 - 25762168
-UGCGGCGGCGCCUCUGGGCGAAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAG--------CCAUA--------CCCGUGC
-.((((.((((((((..(((((....)))))...)))))..((((......(((((((....)))))))......)))).......)--------))...--------.)))).. ( -41.40, z-score =  -1.81, R)
>droYak2.chr3L 4865623 104 + 24197627
CUGCGGCGGCGGCUCUGGGCGAAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAA--------CCAUAA---CAAUCCCGUGC
.((.(((((((...((((((((((.((..(((.((((..((...))..)))).)))))))))))))))..))))))).)).......--------......---........... ( -35.70, z-score =  -0.40, R)
>droSec1.super_11 1147325 106 - 2888827
-CGCGGCGACGCCUCUGGGCGAAAUGUUGUCACCAAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAA--------CCAUACCACCAUACCCAUGC
-.(.((((((((((..((((((....))))).)..))))............(((((((....)))))))..)))))).)........--------.................... ( -35.10, z-score =  -1.53, R)
>droSim1.chr3L 20551739 106 - 22553184
-CGCGGCGACGCCUCUGGGCGAAAUGUUGUCACCAAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCACUUCACCCAUAA--------CCAUACCGCCAUACCCAUGC
-...((((..((((..((((((....))))).)..))))..((((......(((((((....)))))))......))))........--------......)))).......... ( -34.90, z-score =  -1.46, R)
>consensus
_CGCGGCGGCGCCUCUGGGCGAAAUGUUGUCACUGAGGCUCGAAGAUUCUCGCUGGGCUUUCGCCCGGCACGUCGCUUCACCCAUAA________CCAUACC_CCAUACCCAUGC
..((((((..(((((..(((((....)))))...)))))............(((((((....))))))).))))))....................................... (-34.04 = -34.84 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:41:46 2011