Locus 8749

Sequence ID dm3.chr3R
Location 1,251,494 – 1,251,634
Length 140
Max. P 0.874365
window12008 window12009

overview

Window 8

Location 1,251,494 – 1,251,634
Length 140
Sequences 7
Columns 140
Reading direction forward
Mean pairwise identity 61.38
Shannon entropy 0.75659
G+C content 0.60105
Mean single sequence MFE -49.79
Consensus MFE -17.19
Energy contribution -19.61
Covariance contribution 2.42
Combinations/Pair 1.50
Mean z-score -1.45
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874365
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1251494 140 + 27905053
GCAGCUCCAGCUCCAGCUCCUGCUCCUGCUCCCCCGAAAGGAUCCUCCGCUCGGUCAUCAGAGGCGCCCUCCUAUCCCGAUCCUGGAGGCGCUUCUUCUGGAGGUGGUAGCUGCAGGAGCAGGCCUUGCCAUGCUUUUUU
(((((((((.((((((.....((....))....((((..((.....))..)))).....(((((((((.(((............)))))))))))).)))))).))).))))))((((((((((...))).))))))).. ( -64.30, z-score =  -2.85, R)
>droAna3.scaffold_13340 19760435 113 - 23697760
---------------------UCCCAUCCGGCAACGGAUGCCGUCGGCGCUCGGU------GUGCAUCUUCACUUGGUGGUCACCCAAAGGUUUCGGAAACCUUUUCGAGUCGUAGGAGAAGGCCCUGCGAUUCUUGAUC
---------------------...((((((....)))))).......((((.(((------(........)))).))))((((...(((((((.....)))))))..((((((((((.......)))))))))).)))). ( -41.00, z-score =  -1.27, R)
>droEre2.scaffold_4770 1521334 128 + 17746568
------------GUUGCUCCUGCUCCUGCUCCUCCGCAAGGAUCCUUCGCUCGGUCAUCAGAGGCGCCAUCUUAUCCCGAUCCUGGAGGCGCAUUUUCUGGAGGUGGUAGCUGCAAGAGCAGGCCUUGUCAUUCUUCUUC
------------.((((((.(((..(((((((((((((((....))).)).........(((.(((((.(((............))))))))....)))))))).)))))..))).)))))).................. ( -43.80, z-score =  -0.45, R)
>droYak2.chr3R 1649736 122 + 28832112
------------------GCUGCGCAUGCUCCUCCGGAAAGAUCCUUCGCUCGGUCAUCAGAGGCAUCCUCUGAUCUCGAUCCUGGGGACGCUUCGUCUGGAGGUGGUAACUGCAAGAGCAGGCCUUGGCAUUCUUGUUC
------------------(((..((.((((((((((((..((((........))))....(((((.(((((.(((....)))..))))).))))).)))))))).)))).((((....))))))...))).......... ( -45.70, z-score =  -0.88, R)
>droSec1.super_6 1370530 137 + 4358794
GCAGAUCCAGCUCCAGCUCCUGCUCCUGCUCCCUCGAAAGGAUCCUCCGCUCGGUCAUCAGAGGCGCCCUCGUAUCCCGAUUCUGAAGGCGCUUCU---GGAGGUGGUAGCUGCAGGAGCAGGCCUUGCCAUUCUUGUUC
((((...........((((((((..((((..((((((..((.....))..))......((((((((((.(((...........))).)))))))))---)))))..))))..)))))))).(((...)))....)))).. ( -58.90, z-score =  -2.37, R)
>droSim1.chr3R 1250392 137 + 27517382
GCAGAUCCAGCUCCAGCUCCUGCUCCUGCUCCCUCGAAAGGAUCCUCCGCUCGGUCAUCAGAGGCGCCCUCGUAUCCCGAUCCUGAAGGUGCUUCU---GGAGGUGGUAGCUGCAGGAGCAGGCCUUGCCAUUCUUGUUC
((((...........((((((((..((((..((((((..((.....))..))......((((((((((.(((...........))).)))))))))---)))))..))))..)))))))).(((...)))....)))).. ( -57.00, z-score =  -1.99, R)
>anoGam1.chrX 14832065 116 - 22145176
------------GCACCUUCACCUCCAGCUCCUUCUGCAGCUCCGUCCGCUUGAU------GCGCGUGCUCCGCUCCUGCGUCAGCUGGCUCUGCAGC-UCCGCCAGCUCCUGCUGCAGCAUGUCGCG-CAUCGUC----
------------..............((((.(....).))))..........(((------(((((.((...(((.(.(((..(((((((........-...)))))))..))).).)))..))))))-))))...---- ( -37.80, z-score =  -0.33, R)
>consensus
____________CCAGCUCCUGCUCCUGCUCCCCCGAAAGGAUCCUCCGCUCGGUCAUCAGAGGCGCCCUCCUAUCCCGAUCCUGGAGGCGCUUCUUC_GGAGGUGGUAGCUGCAGGAGCAGGCCUUGCCAUUCUUGUUC
..................(((((((.((((((.......))).(((((.(((........)))(((((.((.............)).))))).......)))))........))).)))))))................. (-17.19 = -19.61 +   2.42)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,251,494 – 1,251,634
Length 140
Sequences 7
Columns 140
Reading direction reverse
Mean pairwise identity 61.38
Shannon entropy 0.75659
G+C content 0.60105
Mean single sequence MFE -47.39
Consensus MFE -20.54
Energy contribution -21.14
Covariance contribution 0.60
Combinations/Pair 1.70
Mean z-score -0.51
Structure conservation index 0.43
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.chr3R 1251494 140 - 27905053
AAAAAAGCAUGGCAAGGCCUGCUCCUGCAGCUACCACCUCCAGAAGAAGCGCCUCCAGGAUCGGGAUAGGAGGGCGCCUCUGAUGACCGAGCGGAGGAUCCUUUCGGGGGAGCAGGAGCAGGAGCUGGAGCUGGAGCUGC
.....(((.((((.((.(((((((((((.(....).(((((..(((.....(((((....((((....(((((...))))).....))))..)))))...)))..))))).)))))))))))..))...))))..))).. ( -61.40, z-score =  -0.94, R)
>droAna3.scaffold_13340 19760435 113 + 23697760
GAUCAAGAAUCGCAGGGCCUUCUCCUACGACUCGAAAAGGUUUCCGAAACCUUUGGGUGACCACCAAGUGAAGAUGCAC------ACCGAGCGCCGACGGCAUCCGUUGCCGGAUGGGA---------------------
......((.(((.((((.....)))).))).))..(((((((.....)))))))((....)).(((.(((......)))------.(((.((...(((((...)))))))))).)))..--------------------- ( -33.40, z-score =   0.36, R)
>droEre2.scaffold_4770 1521334 128 - 17746568
GAAGAAGAAUGACAAGGCCUGCUCUUGCAGCUACCACCUCCAGAAAAUGCGCCUCCAGGAUCGGGAUAAGAUGGCGCCUCUGAUGACCGAGCGAAGGAUCCUUGCGGAGGAGCAGGAGCAGGAGCAAC------------
.................(((((((((((.((.................)).(((((....((((....(((.(....)))).....))))((.(((....)))))))))).)))))))))))......------------ ( -43.53, z-score =  -0.87, R)
>droYak2.chr3R 1649736 122 - 28832112
GAACAAGAAUGCCAAGGCCUGCUCUUGCAGUUACCACCUCCAGACGAAGCGUCCCCAGGAUCGAGAUCAGAGGAUGCCUCUGAUGACCGAGCGAAGGAUCUUUCCGGAGGAGCAUGCGCAGC------------------
......(.((((...((.((((....))))...)).(((((.((((...))))....(((..((.((((((((...))))))))..((.......)).))..)))))))).)))).).....------------------ ( -39.30, z-score =  -0.63, R)
>droSec1.super_6 1370530 137 - 4358794
GAACAAGAAUGGCAAGGCCUGCUCCUGCAGCUACCACCUCC---AGAAGCGCCUUCAGAAUCGGGAUACGAGGGCGCCUCUGAUGACCGAGCGGAGGAUCCUUUCGAGGGAGCAGGAGCAGGAGCUGGAGCUGGAUCUGC
.....(((.((((.((.(((((((((((........(((((---....((((((((.............))))))))(((........))).))))).((((.....)))))))))))))))..))...))))..))).. ( -58.12, z-score =  -1.61, R)
>droSim1.chr3R 1250392 137 - 27517382
GAACAAGAAUGGCAAGGCCUGCUCCUGCAGCUACCACCUCC---AGAAGCACCUUCAGGAUCGGGAUACGAGGGCGCCUCUGAUGACCGAGCGGAGGAUCCUUUCGAGGGAGCAGGAGCAGGAGCUGGAGCUGGAUCUGC
.....(((.((((.((.(((((((((((........(((((---.((((...))))....((((.....((((...))))......))))..))))).((((.....)))))))))))))))..))...))))..))).. ( -54.20, z-score =  -0.68, R)
>anoGam1.chrX 14832065 116 + 22145176
----GACGAUG-CGCGACAUGCUGCAGCAGGAGCUGGCGGA-GCUGCAGAGCCAGCUGACGCAGGAGCGGAGCACGCGC------AUCAAGCGGACGGAGCUGCAGAAGGAGCUGGAGGUGAAGGUGC------------
----...((((-((((...((((.(.((...(((((((...-........)))))))...)).).)))).....)))))------)))..(((..(...(((.(((......)))..)))...).)))------------ ( -41.80, z-score =   0.80, R)
>consensus
GAACAAGAAUGGCAAGGCCUGCUCCUGCAGCUACCACCUCC_GAAGAAGCGCCUCCAGGAUCGGGAUAAGAGGGCGCCUCUGAUGACCGAGCGGAGGAUCCUUCCGAAGGAGCAGGAGCAGGAGCUGG____________
..................((((((((((....................((((((.................)))))).....................((((.....))))))))))))))................... (-20.54 = -21.14 +   0.60)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:51:24 2011