Locus 3305

Sequence ID	dm3.chr2R
Location	4,246,113 – 4,246,204
Length	91
Max. P	0.754893

overview

Window 2

Location	4,246,113 – 4,246,204
Length	91
Sequences	7
Columns	115
Reading direction	forward
Mean pairwise identity	61.93
Shannon entropy	0.67733
G+C content	0.56826
Mean single sequence MFE	-25.67
Consensus MFE	-10.54
Energy contribution	-10.86
Covariance contribution	0.32
Combinations/Pair	1.67
Mean z-score	-1.18
Structure conservation index	0.41
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.59
SVM RNA-class probability	0.754893
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4246113 91 + 21146708
GUUUUGGUCCUCCCUACUAAGGGGCUUCAGCUCACGUCAGAGC---------------GGCUCCUCGAAUAAACCCCCAAAACCUCCAAGUCCACCGAAGCCACCA---------
....((((....(((....)))((((((.((((......))))---------------((((..........................))))....))))))))))--------- ( -21.47, z-score =  -1.13, R)
>droWil1.scaffold_180701 676607 72 + 3904529
GUUCCGACCAGCCAUA--AACGCACUUGAGACGACGGCACGCA--------------UGCAUGGUGGUCGAAACUAUGGCAAUUCCUA---------------------------
(((.((((((.((((.--..(((......).))...(((....--------------))))))))))))).)))..............--------------------------- ( -17.80, z-score =  -0.22, R)
>droAna3.scaffold_13266 18135252 109 - 19884421
GUUUUGGUCAACACUUAGCCGGGCCUUCACCAGGCGACAGAACUCCUCAGCAUCUGCUGGUCCGCCAAAGAAGCCAUCGGGAUCCGAUGGUCCGCCAAAGCCACCGGGA------
((((((((.....(((.(.(((((((.....))))...........(((((....))))).))).).)))..((((((((...))))))))..))))))))........------ ( -36.30, z-score =  -0.39, R)
>droEre2.scaffold_4929 8254090 100 - 26641161
GUUUUGGUCCUCCCUUUUAAGGGGCUUCAGCUCACGUCAGAGC---------------GGCUCCUCAAGUAAGCCCCCCAAGCCUCCAAAUCCUCCACAUCCGCCGAAGCCGCCA
((((((((....(((....)))(((((..((((......))))---------------((((.........))))....)))))..................))))))))..... ( -26.10, z-score =  -1.54, R)
>droYak2.chr2L 16901808 91 + 22324452
GUUUUGGUCCUCUUUAUUAAGGGGCUUCAGCUCACGUAAGAGC---------------GGCUCCUCAAGCAAGCCCCCAAAGCCUCCAAAUCCACCGAAGCCUCCA---------
((((((((............(((((((..((((......))))---------------.(((.....))))))))))................)))))))).....--------- ( -25.99, z-score =  -2.07, R)
>droSec1.super_1 1892151 91 + 14215200
GUUUUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGC---------------GGCUCCUCGAAUAAGCCCCCAAAGCCUCCAAGUCCACCGAAGCCGCCA---------
((((((((....(((....)))(((((..((((......))))---------------((((.........))))....))))).........)))))))).....--------- ( -26.00, z-score =  -1.46, R)
>droSim1.chr2R_random 1382531 91 + 2996586
GUUUUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGC---------------GGCUCCUCGAAUAAGCCCCCAAAGCCUCCAAGUCCACCGAAGCCGCCA---------
((((((((....(((....)))(((((..((((......))))---------------((((.........))))....))))).........)))))))).....--------- ( -26.00, z-score =  -1.46, R)
>consensus
GUUUUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGC_______________GGCUCCUCGAAUAAGCCCCCAAAGCCUCCAAGUCCACCGAAGCCGCCA_________
(((((((............(((((((...((((......))))...............)))))))...........)))))))................................ (-10.54 = -10.86 +   0.32)

alignment

secondary structure

dotplot

Window 3

Location	4,246,113 – 4,246,204
Length	91
Sequences	7
Columns	115
Reading direction	reverse
Mean pairwise identity	61.93
Shannon entropy	0.67733
G+C content	0.56826
Mean single sequence MFE	-34.13
Consensus MFE	-12.62
Energy contribution	-13.12
Covariance contribution	0.50
Combinations/Pair	1.67
Mean z-score	-1.29
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.35
SVM RNA-class probability	0.655744
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4246113 91 - 21146708
---------UGGUGGCUUCGGUGGACUUGGAGGUUUUGGGGGUUUAUUCGAGGAGCC---------------GCUCUGACGUGAGCUGAAGCCCCUUAGUAGGGAGGACCAAAAC
---------(((((((((((((..(((..((((((((..(((....)))..))))))---------------..))..).))..)))))))))((((......)))))))).... ( -32.30, z-score =  -1.00, R)
>droWil1.scaffold_180701 676607 72 - 3904529
---------------------------UAGGAAUUGCCAUAGUUUCGACCACCAUGCA--------------UGCGUGCCGUCGUCUCAAGUGCGUU--UAUGGCUGGUCGGAAC
---------------------------..((.....))...(((((((((((((((..--------------.(((..(...........)..))).--))))).)))))))))) ( -26.10, z-score =  -2.29, R)
>droAna3.scaffold_13266 18135252 109 + 19884421
------UCCCGGUGGCUUUGGCGGACCAUCGGAUCCCGAUGGCUUCUUUGGCGGACCAGCAGAUGCUGAGGAGUUCUGUCGCCUGGUGAAGGCCCGGCUAAGUGUUGACCAAAAC
------....(((((((((.((((((((((((...))))))).)))...(((((..((((....)))).((....)).)))))..)).))))))((((.....)))))))..... ( -40.40, z-score =  -0.35, R)
>droEre2.scaffold_4929 8254090 100 + 26641161
UGGCGGCUUCGGCGGAUGUGGAGGAUUUGGAGGCUUGGGGGGCUUACUUGAGGAGCC---------------GCUCUGACGUGAGCUGAAGCCCCUUAAAAGGGAGGACCAAAAC
(((.(((((((((..((((((((....(((...((..((.......))..))...))---------------))))).))))..)))))))))((((......)))).))).... ( -37.10, z-score =  -1.26, R)
>droYak2.chr2L 16901808 91 - 22324452
---------UGGAGGCUUCGGUGGAUUUGGAGGCUUUGGGGGCUUGCUUGAGGAGCC---------------GCUCUUACGUGAGCUGAAGCCCCUUAAUAAAGAGGACCAAAAC
---------(((.(((((((...........((((((..(((....)))..))))))---------------((((......)))))))))))((((......)))).))).... ( -33.00, z-score =  -1.39, R)
>droSec1.super_1 1892151 91 - 14215200
---------UGGCGGCUUCGGUGGACUUGGAGGCUUUGGGGGCUUAUUCGAGGAGCC---------------GCUCUGACGUGAGCUGAAGCCCCUUAAUAGGGAGGACCAAAAC
---------(((.(((((((((...((((((((((.....))))..))))))..)))---------------((((......)))).))))))((((......)))).))).... ( -35.00, z-score =  -1.36, R)
>droSim1.chr2R_random 1382531 91 - 2996586
---------UGGCGGCUUCGGUGGACUUGGAGGCUUUGGGGGCUUAUUCGAGGAGCC---------------GCUCUGACGUGAGCUGAAGCCCCUUAAUAGGGAGGACCAAAAC
---------(((.(((((((((...((((((((((.....))))..))))))..)))---------------((((......)))).))))))((((......)))).))).... ( -35.00, z-score =  -1.36, R)
>consensus
_________UGGCGGCUUCGGUGGACUUGGAGGCUUUGGGGGCUUAUUCGAGGAGCC_______________GCUCUGACGUGAGCUGAAGCCCCUUAAUAGGGAGGACCAAAAC
..........((.(((((((((........(((((.....)))))......(((((................))))).......))))))))))).................... (-12.62 = -13.12 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:07:46 2011