Locus 13465

Sequence ID	dm3.chrX
Location	6,716,939 – 6,717,054
Length	115
Max. P	0.983982

overview

Window 6

Location	6,716,939 – 6,717,054
Length	115
Sequences	10
Columns	116
Reading direction	forward
Mean pairwise identity	61.78
Shannon entropy	0.78702
G+C content	0.57710
Mean single sequence MFE	-38.73
Consensus MFE	-18.54
Energy contribution	-18.64
Covariance contribution	0.10
Combinations/Pair	1.00
Mean z-score	-1.22
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.15
SVM RNA-class probability	0.983982
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6716939 115 + 22422827
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC-UGGACGGGAUUCUCUGGUCCGAUCGGCACAAUGGACAACGAACAAUGGCUGUUAAGCAGAAUUCGGUGGGCAGGUAGCGGU
...(((((((.((((((((((((((((..((((.-(((((.((.....)).)))))..)))).(....)....)))))..))))))))..)).(....)....).))))).))... ( -44.70, z-score =  -1.17, R)
>droSim1.chrX 5271859 115 + 17042790
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC-UGGCCAGGAUUCUCUGGUCCGAUCGGCACAAUGGACAACGAACAAUGGCUGUUAAGCGGAAUUCGGUGGGCAGGUAGCGAU
...(((((((.(..(((((((((((((..((((.-(((((.((((......))))....))).)).))).)..)))))..))))))))..((.(....).)).).))))).))... ( -44.90, z-score =  -0.94, R)
>droSec1.super_4 6100052 115 - 6179234
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC-UGGCCAGGAUUCUCUGGUCCGAUCGGCACAAUGGACAACGAACAAUGGCUGUUAAGCGGAAUUCGGUGGGCAGGUAGCGAU
...(((((((.(..(((((((((((((..((((.-(((((.((((......))))....))).)).))).)..)))))..))))))))..((.(....).)).).))))).))... ( -44.90, z-score =  -0.94, R)
>droYak2.chrX 2684420 113 + 21770863
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC-UGGCCAGGAUUCUCUGGUCCAAACA--ACAAUGGACAACGAACAAUGGCUGUUAAACGGAAUUCGGUGGGCAGGUAGCGAU
..((((((((((......))))....))))))((-(.(((.(((((((...(((((....--....)))))....((((.....))))....)))))))))).))).......... ( -43.20, z-score =  -1.87, R)
>droEre2.scaffold_4690 15644880 115 + 18748788
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC-UGGCCGGGAUUCUCUGGACCAAACAACACAAUGGACAACGAACAAUGGCUGUUAAGCGGAAUUCGAUGGGCAGGUAGCGAU
..((((((((((......))))....))))))((-((((((((....))))).)).....((....((..((.((((...(.(((....))).)..)))).))..)).)))))... ( -39.50, z-score =  -0.72, R)
>droAna3.scaffold_13117 516874 93 + 5790199
AAGGCGCCUGGGGCAACAGCCAGCACGGCGCCGC-UGGCUGGGAUGAU-------AAACAAUGCC-UGCGCCAUAAACAAAAGGCGUUAAGCGGAAAUCGUC--------------
..(((((...(((((.((((((((........))-))))))...((..-------...)).))))-))))))...........((.....))..........-------------- ( -33.70, z-score =  -0.70, R)
>dp4.chrXL_group1a 6546084 103 + 9151740
AAGGCGCCUGGCGCAACAGCCAGCUCGGCGCCGCAUCUUCGAAGCGAGC-----CAAACAAUGGCUCAAACUAUUAA--GUGGAAACCGACCGAUCCUAGGUACAACGCU------
..((((((((((......))))....))))))((.((...)).))((((-----((.....)))))).........(--(((.......(((.......)))....))))------ ( -35.20, z-score =  -1.81, R)
>droPer1.super_25 680749 103 - 1448063
AAGGCGCCUGGCGCAACAGCCAGCUCGGCGCCGCAUCUUCGAAGCGAGC-----CAAACAAUGGCUCAAACUAUUAA--GUGGAAACCGACCGAUCCUAGGUACAACGCU------
..((((((((((......))))....))))))((.((...)).))((((-----((.....)))))).........(--(((.......(((.......)))....))))------ ( -35.20, z-score =  -1.81, R)
>droWil1.scaffold_180777 1900099 89 + 4753960
AAGGCGCCUGGCGCACUAGCCAUGUCGGCGCCGC-UUGCCGCAGCUAA-------AGAUAAUA-CAAUGGCUAUUAA--GCGGAAACCUCUCGAA--UAGAU--------------
..((((((((((......))))....))))))..-...(((((((((.-------.(......-)..))))).....--))))............--.....-------------- ( -27.40, z-score =  -0.26, R)
>droVir3.scaffold_12928 3697743 94 - 7717345
AAGGCGCCUGGCGCAACAGCCAAAUCGGCGCCGA-CUGUCGACUGCCGCUGGGCGAGUCAAUACAAUGGCUGUUAAGCGGAAACC--UAGGUAGCAC-------------------
..((((((((((......))))....))))))..-.....(.((((((((..((.(((((......)))))))..)))(....).--..))))))..------------------- ( -38.60, z-score =  -1.97, R)
>consensus
AAGGCGCCUGGCGCAACAGCCAGUUCGGCGCCGC_UGGCCGGGAUUCUCUGG_CCAAACAAUACAAUGGACAACGAACAAUGGCUGUUAAGCGGAAUUCGGUGGGCAGGU______
..((((((((((......))))....)))))).................................................................................... (-18.54 = -18.64 +   0.10)

alignment

secondary structure

dotplot

Window 7

Location	6,716,939 – 6,717,054
Length	115
Sequences	10
Columns	116
Reading direction	reverse
Mean pairwise identity	61.78
Shannon entropy	0.78702
G+C content	0.57710
Mean single sequence MFE	-36.39
Consensus MFE	-17.42
Energy contribution	-17.52
Covariance contribution	0.10
Combinations/Pair	1.00
Mean z-score	-0.94
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.60
SVM RNA-class probability	0.954287
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6716939 115 - 22422827
ACCGCUACCUGCCCACCGAAUUCUGCUUAACAGCCAUUGUUCGUUGUCCAUUGUGCCGAUCGGACCAGAGAAUCCCGUCCA-GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
...((..((((......(....).((.(((((((((..(((((.........((((((...((((..(.....)..)))).-.)))))))))))))))))))).)))))).))... ( -38.40, z-score =  -1.60, R)
>droSim1.chrX 5271859 115 - 17042790
AUCGCUACCUGCCCACCGAAUUCCGCUUAACAGCCAUUGUUCGUUGUCCAUUGUGCCGAUCGGACCAGAGAAUCCUGGCCA-GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
...((..((((......(.....)((.(((((((((..(((((.........((((((...((.((((......)))))).-.)))))))))))))))))))).)))))).))... ( -42.10, z-score =  -1.94, R)
>droSec1.super_4 6100052 115 + 6179234
AUCGCUACCUGCCCACCGAAUUCCGCUUAACAGCCAUUGUUCGUUGUCCAUUGUGCCGAUCGGACCAGAGAAUCCUGGCCA-GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
...((..((((......(.....)((.(((((((((..(((((.........((((((...((.((((......)))))).-.)))))))))))))))))))).)))))).))... ( -42.10, z-score =  -1.94, R)
>droYak2.chrX 2684420 113 - 21770863
AUCGCUACCUGCCCACCGAAUUCCGUUUAACAGCCAUUGUUCGUUGUCCAUUGU--UGUUUGGACCAGAGAAUCCUGGCCA-GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
...(((.........((((((..((....(((((........)))))....)).--.)))))).((((......))))..)-))((((((....((((......)))))))))).. ( -36.90, z-score =  -1.19, R)
>droEre2.scaffold_4690 15644880 115 - 18748788
AUCGCUACCUGCCCAUCGAAUUCCGCUUAACAGCCAUUGUUCGUUGUCCAUUGUGUUGUUUGGUCCAGAGAAUCCCGGCCA-GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
...((..((((......(.....)((.(((((((((..(((((.........((((((((.((((..(.....)..)))))-))))))))))))))))))))).)))))).))... ( -35.90, z-score =  -0.41, R)
>droAna3.scaffold_13117 516874 93 - 5790199
--------------GACGAUUUCCGCUUAACGCCUUUUGUUUAUGGCGCA-GGCAUUGUUU-------AUCAUCCCAGCCA-GCGGCGCCGUGCUGGCUGUUGCCCCAGGCGCCUU
--------------(((((.....((.....))...)))))...(((((.-((((.((...-------..))...((((((-(((......))))))))).))))....))))).. ( -31.70, z-score =  -0.61, R)
>dp4.chrXL_group1a 6546084 103 - 9151740
------AGCGUUGUACCUAGGAUCGGUCGGUUUCCAC--UUAAUAGUUUGAGCCAUUGUUUG-----GCUCGCUUCGAAGAUGCGGCGCCGAGCUGGCUGUUGCGCCAGGCGCCUU
------.((((........(((..........))).(--((...(((..((((((.....))-----)))))))...)))))))((((((....((((......)))))))))).. ( -36.80, z-score =  -0.36, R)
>droPer1.super_25 680749 103 + 1448063
------AGCGUUGUACCUAGGAUCGGUCGGUUUCCAC--UUAAUAGUUUGAGCCAUUGUUUG-----GCUCGCUUCGAAGAUGCGGCGCCGAGCUGGCUGUUGCGCCAGGCGCCUU
------.((((........(((..........))).(--((...(((..((((((.....))-----)))))))...)))))))((((((....((((......)))))))))).. ( -36.80, z-score =  -0.36, R)
>droWil1.scaffold_180777 1900099 89 - 4753960
--------------AUCUA--UUCGAGAGGUUUCCGC--UUAAUAGCCAUUG-UAUUAUCU-------UUAGCUGCGGCAA-GCGGCGCCGACAUGGCUAGUGCGCCAGGCGCCUU
--------------.(((.--....))).((((((((--.....(((.(..(-......).-------.).))))))).))-))((((((....((((......)))))))))).. ( -27.40, z-score =   0.31, R)
>droVir3.scaffold_12928 3697743 94 + 7717345
-------------------GUGCUACCUA--GGUUUCCGCUUAACAGCCAUUGUAUUGACUCGCCCAGCGGCAGUCGACAG-UCGGCGCCGAUUUGGCUGUUGCGCCAGGCGCCUU
-------------------(((((.....--((...))((.(((((((((.....((((((.(((....))))))))).((-(((....)))))))))))))).))..)))))... ( -35.80, z-score =  -1.34, R)
>consensus
______ACCUGCCCACCGAAUUCCGCUUAACAGCCAUUGUUCAUUGUCCAUUGUAUUGUUUGG_CCAGAGAAUCCCGGCCA_GCGGCGCCGAACUGGCUGUUGCGCCAGGCGCCUU
....................................................................................((((((....((((......)))))))))).. (-17.42 = -17.52 +   0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:59 2011