Locus 822

Sequence ID	dm3.chr2L
Location	5,967,062 – 5,967,162
Length	100
Max. P	0.865425

overview

Window 4

Location	5,967,062 – 5,967,162
Length	100
Sequences	10
Columns	109
Reading direction	forward
Mean pairwise identity	58.96
Shannon entropy	0.79653
G+C content	0.55170
Mean single sequence MFE	-33.65
Consensus MFE	-13.62
Energy contribution	-12.78
Covariance contribution	-0.84
Combinations/Pair	1.33
Mean z-score	-1.02
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.97
SVM RNA-class probability	0.865425
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5967062 100 + 23011544
AUGACCCGCCCUCAAAGGCGGGAAACACGGGAAAGUUGUG----ACCGUAAUCAUGAUGUUCAGCGGGUUGAGGAUUAAA--CGGAGGCAUAUGCUCCAUGGAGGG---
....((((((......))))))...(((((.....)))))----.((((.....((((.(((((....))))).))))..--.((((.(....)))))))))....--- ( -30.60, z-score =  -0.59, R)
>droSim1.chr2L 5755037 100 + 22036055
AUGACCCGCCCUCAUAGGCGGGAAACACGGGAAAGUUGUG----ACCGAAAUCAUGAUGUUCAGCGGGUUGAGGGUUAAA--CGGAGGCAUAUGCUCCAUGGAGGG---
....((((((((((...((.(....)....(((.((..((----(......)))..)).))).))....)))))))....--.((((.(....))))).....)))--- ( -31.50, z-score =  -0.63, R)
>droSec1.super_5 4038020 100 + 5866729
AUGACCCGCCCUCAUAGGCGGGAAACACGGGAAAGUUGUG----ACCGAAAUCAUGAUGUUCAGCGGGUUGAGGGUUAAA--CGGAGGCAUAUGCUCCAUGGAGGG---
....((((((((((...((.(....)....(((.((..((----(......)))..)).))).))....)))))))....--.((((.(....))))).....)))--- ( -31.50, z-score =  -0.63, R)
>droYak2.chr2L 9096599 100 - 22324452
AUGACCCGCCCUCAAAGGCGGGAAACACGGGAAAGUUGUG----ACCGGAAUCAUGGUGUACUGCGGGCUGAGGAUUUAA--CGGAGGCAUAUGCUCCAUGGAGGG---
....((((((......))))))...(((((.....)))))----.((....((((((.(((.(((...(((.........--)))..)))..))).)))))).)).--- ( -30.00, z-score =   0.12, R)
>droEre2.scaffold_4929 6057372 100 + 26641161
AUGACCCGCCCUCAAAGGCGGGAAACACGGGAAAGUUGUG----ACCGGCAUCGUGGUGUACAGCGGGUUGAGGGUUUAA--CAGAGGCAUGUGCUCCAUGGAGGG---
....((((((......))))))...(((((.....)))))----.((....((((((.(((((((..(((((....))))--)....)).))))).)))))).)).--- ( -34.80, z-score =  -0.65, R)
>dp4.chr4_group1 4960429 109 - 5278887
AUAACCCGCCUCCAAAGGCGGGAAACGAUGGAAAGGUAUGGGCAAUCGGUGCAGCUUGUUGUUGAUAGCCAGGUGCCACAGCUGGUGGCGCCUGCUUCUGGGAAGGAAA
....(((((((....))))))).......((((.(.(((.((((((.((.....)).)))))).))).)((((((((((.....)))))))))).)))).......... ( -43.70, z-score =  -1.60, R)
>droPer1.super_1 9968913 109 - 10282868
AUAACCCGCCUCCAAAGGCGGGAAACGAUGGAAAGGUAUGGGCAAUCGGUGCAGCUUGUUGUUGAUAGCCAGGUGCCACAGCUGGUGGCGCCUGCUUCUGGGAAGGAAA
....(((((((....))))))).......((((.(.(((.((((((.((.....)).)))))).))).)((((((((((.....)))))))))).)))).......... ( -43.70, z-score =  -1.60, R)
>droVir3.scaffold_12963 3251851 88 + 20206255
AAAACCCAGCGCCAAAGCUGGGAAACGAUGGAAA------------CGGCGCCUGAGCAUAUUGGCCAUUCAUGGGCAUCGGCUGUGCCUCUGGCUGCGG---------
....((((((......))))))......((....------------))(((((.(((((((.((.(((....))).)).....)))).))).))).))..--------- ( -32.60, z-score =  -0.62, R)
>droMoj3.scaffold_6500 13615475 88 + 32352404
AAAACCCAGCUCCAAAGCUGGGAAACGACGGAAA------------CGGCGUCUGAAUAUACUGCGGACUAAUGGGCCUCGCUUGUUGCUCCGUCUGUUG---------
....(((((((....)))))))...(((((((..------------.((((((((.........))))).((..(((...)))..)))))...)))))))--------- ( -32.20, z-score =  -3.33, R)
>droGri2.scaffold_15252 2836769 88 + 17193109
GAAACCCAGCCCCAAAGCUGGGAAACGAUGGAAA------------UGGCACCGAUGCAUACUGUACAUUUAUUGGCAUCGCUUGUCCAGCUGGCUGUGC---------
......(((((....(((((((...(((((....------------..(((....)))........((.....)).)))))....))))))))))))...--------- ( -25.90, z-score =  -0.65, R)
>consensus
AUAACCCGCCCCCAAAGGCGGGAAACAAGGGAAAGUUGUG____ACCGGAAUCAUGAUGUACUGCGGGUUGAGGGUCAAA__CGGAGGCACAUGCUCCAUGGAGGG___
....((((((......))))))....................................................................................... (-13.62 = -12.78 +  -0.84)

alignment

secondary structure

dotplot

Window 5

Location	5,967,062 – 5,967,162
Length	100
Sequences	10
Columns	109
Reading direction	reverse
Mean pairwise identity	58.96
Shannon entropy	0.79653
G+C content	0.55170
Mean single sequence MFE	-26.80
Consensus MFE	-13.65
Energy contribution	-12.73
Covariance contribution	-0.92
Combinations/Pair	1.43
Mean z-score	-0.41
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.87
SVM RNA-class probability	0.839809
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5967062 100 - 23011544
---CCCUCCAUGGAGCAUAUGCCUCCG--UUUAAUCCUCAACCCGCUGAACAUCAUGAUUACGGU----CACAACUUUCCCGUGUUUCCCGCCUUUGAGGGCGGGUCAU
---........(((((....).))))(--((((.............)))))...((((.(((((.----..........)))))...(((((((....))))))))))) ( -24.62, z-score =  -0.41, R)
>droSim1.chr2L 5755037 100 - 22036055
---CCCUCCAUGGAGCAUAUGCCUCCG--UUUAACCCUCAACCCGCUGAACAUCAUGAUUUCGGU----CACAACUUUCCCGUGUUUCCCGCCUAUGAGGGCGGGUCAU
---(((...(((((((....).)))))--)....((((((...((..((((((...((....(((----....))).))..))))))..))....)))))).))).... ( -24.10, z-score =  -0.17, R)
>droSec1.super_5 4038020 100 - 5866729
---CCCUCCAUGGAGCAUAUGCCUCCG--UUUAACCCUCAACCCGCUGAACAUCAUGAUUUCGGU----CACAACUUUCCCGUGUUUCCCGCCUAUGAGGGCGGGUCAU
---(((...(((((((....).)))))--)....((((((...((..((((((...((....(((----....))).))..))))))..))....)))))).))).... ( -24.10, z-score =  -0.17, R)
>droYak2.chr2L 9096599 100 + 22324452
---CCCUCCAUGGAGCAUAUGCCUCCG--UUAAAUCCUCAGCCCGCAGUACACCAUGAUUCCGGU----CACAACUUUCCCGUGUUUCCCGCCUUUGAGGGCGGGUCAU
---......(((((((....).)))))--)..........(.(((.(((........))).))).----)...........(((...(((((((....))))))).))) ( -24.20, z-score =  -0.00, R)
>droEre2.scaffold_4929 6057372 100 - 26641161
---CCCUCCAUGGAGCACAUGCCUCUG--UUAAACCCUCAACCCGCUGUACACCACGAUGCCGGU----CACAACUUUCCCGUGUUUCCCGCCUUUGAGGGCGGGUCAU
---.....(((((.((....)).....--...........(((.((.............)).)))----..........)))))...(((((((....))))))).... ( -23.62, z-score =   0.56, R)
>dp4.chr4_group1 4960429 109 + 5278887
UUUCCUUCCCAGAAGCAGGCGCCACCAGCUGUGGCACCUGGCUAUCAACAACAAGCUGCACCGAUUGCCCAUACCUUUCCAUCGUUUCCCGCCUUUGGAGGCGGGUUAU
...........((((((((.(((((.....))))).)))(((.(((................))).)))..............)))))((((((....))))))..... ( -32.69, z-score =  -0.84, R)
>droPer1.super_1 9968913 109 + 10282868
UUUCCUUCCCAGAAGCAGGCGCCACCAGCUGUGGCACCUGGCUAUCAACAACAAGCUGCACCGAUUGCCCAUACCUUUCCAUCGUUUCCCGCCUUUGGAGGCGGGUUAU
...........((((((((.(((((.....))))).)))(((.(((................))).)))..............)))))((((((....))))))..... ( -32.69, z-score =  -0.84, R)
>droVir3.scaffold_12963 3251851 88 - 20206255
---------CCGCAGCCAGAGGCACAGCCGAUGCCCAUGAAUGGCCAAUAUGCUCAGGCGCCG------------UUUCCAUCGUUUCCCAGCUUUGGCGCUGGGUUUU
---------.....(((...))).....(((((.....(((((((......((....))))))------------))).)))))...((((((......)))))).... ( -24.90, z-score =   1.32, R)
>droMoj3.scaffold_6500 13615475 88 - 32352404
---------CAACAGACGGAGCAACAAGCGAGGCCCAUUAGUCCGCAGUAUAUUCAGACGCCG------------UUUCCGUCGUUUCCCAGCUUUGGAGCUGGGUUUU
---------.....((((((((.....(((.(((......)))))).((........))...)------------.)))))))....(((((((....))))))).... ( -29.10, z-score =  -2.63, R)
>droGri2.scaffold_15252 2836769 88 - 17193109
---------GCACAGCCAGCUGGACAAGCGAUGCCAAUAAAUGUACAGUAUGCAUCGGUGCCA------------UUUCCAUCGUUUCCCAGCUUUGGGGCUGGGUUUC
---------...(((((((((((..((((((((.....((((((((.(.......).))).))------------))).)))))))).))))))....)))))...... ( -28.00, z-score =  -0.90, R)
>consensus
___CCCUCCAUGGAGCAUAUGCCACCG__UUUAACCCUCAACCCGCAGUACACCACGAUGCCGGU____CACAACUUUCCCGCGUUUCCCGCCUUUGAGGGCGGGUCAU
.......................................................................................(((((((....))))))).... (-13.65 = -12.73 +  -0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:20:11 2011