Locus 4618

Sequence ID dm3.chr2R
Location 14,601,331 – 14,601,470
Length 139
Max. P 0.899394
window6334 window6335

overview

Window 4

Location 14,601,331 – 14,601,470
Length 139
Sequences 6
Columns 140
Reading direction forward
Mean pairwise identity 72.87
Shannon entropy 0.50627
G+C content 0.52031
Mean single sequence MFE -42.15
Consensus MFE -23.75
Energy contribution -25.42
Covariance contribution 1.67
Combinations/Pair 1.27
Mean z-score -1.10
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.612212
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14601331 139 + 21146708
CACCCCCUCCCCCCCACGGAGAAAAGCAUUCGGCGAAUA-GUGAUGCAAAUGCAACUUCAGUUGACACUGCACCUGCAUCGUGGAUUUCGCUGCAAUGUAGCACUUUGUACAUUUGCAGCUGUGUCGAGUGAUAGGCAGC
..((..((((.......)))).....(((((((((((..-((((((((..((((...((....))...))))..))))))))....)))(((((((((((........)))).)))))))...))))))))...)).... ( -43.40, z-score =  -1.34, R)
>droSim1.chr2R 13311425 136 + 19596830
CCCCCAACCCACCCCCCGGAGAAAAGCAUUCGGCGCAUA-GUGAUGCAAAUGCAACUUCAGUUGACACUGCACCUGCAUCGUGGAUUUCGCUGCAAUGUAGCACUUUGUACAUUUGCAGCUGUGUCGAGUGAUAGGC---
...((...((.......)).......(((((((((((..-..((((((..((((...((....))...))))..)))))).........(((((((((((........)))).))))))))))))))))))...)).--- ( -43.60, z-score =  -1.70, R)
>droSec1.super_1 12109114 124 + 14215200
------------CCCCCGUAGAAAAGCAUUCGGCGCAUA-GUGAUGCAAAUGCAACUCCAGUUGACACUGCACCUGCAUCGUGGAUUUCGCUGCACUGUAGCACUUUGUACAUUUGCAGCUGUGUCGAGUGAUAGGC---
------------..............(((((((((((..-..((((((..((((..((.....))...))))..)))))).........((((((.((((........))))..)))))))))))))))))......--- ( -38.80, z-score =  -0.55, R)
>droYak2.chr2R 6540709 131 - 21139217
------CCCUCCCCCGCCGAGUGAAGCAUUCGGGGAAAAAGCGUUGCAAAUGCAACUUCAGUUGACACUGCACCUGCAGCAAGAAUUUCGCUGCAAUGUGGCACUUUGUACAUUUGCAGCUGUGUCGAGUGAUAGGC---
------.(((...((.(((((((...))))))))).......(((((....))))).(((.((((((((((....)))...........(((((((((((.(.....))))).))))))).))))))).))).))).--- ( -46.40, z-score =  -1.83, R)
>droEre2.scaffold_4845 8792556 129 + 22589142
-------CCCCCUCCGCCAGGAGAAGCGUUCGGGGAGAA-GUGAUGCAAAUGCAACUCCAGUUGACACUGCACCUGCAGCAAGGAUUUCGCUGCAAUGUAGCACUUUGUGCACUUGCAGCUGUGUCGAGUGAUAGGC---
-------((((((((....))))........))))....-....(((....)))....((.(((((((....(((......))).....(((((((.((.((((...))))))))))))).))))))).))......--- ( -44.40, z-score =  -0.47, R)
>droAna3.scaffold_13266 2108002 117 - 19884421
----------------CAAAAACAGGGGCCUGCAUCCAAGGGGUAGCCAAUGCAAAUGCAACUGCCUCUGCCUCUGC--CACAGAUGCCAAAAGGAAAAAGAA--UACUAGAAUUGCGGCAGUGGCAACUGAUAGGC---
----------------...........(((((((....((((((((....(((....))).))))))))(((.((((--(.(((...((....))....((..--..))....))).))))).)))...)).)))))--- ( -36.30, z-score =  -0.68, R)
>consensus
_______CCCCCCCCCCGGAGAAAAGCAUUCGGCGAAAA_GUGAUGCAAAUGCAACUUCAGUUGACACUGCACCUGCAUCAUGGAUUUCGCUGCAAUGUAGCACUUUGUACAUUUGCAGCUGUGUCGAGUGAUAGGC___
..........................(((((((.........((((((..((((...((....))...))))..)))))).........(((((((((((........)))).)))))))....)))))))......... (-23.75 = -25.42 +   1.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,601,331 – 14,601,470
Length 139
Sequences 6
Columns 140
Reading direction reverse
Mean pairwise identity 72.87
Shannon entropy 0.50627
G+C content 0.52031
Mean single sequence MFE -45.64
Consensus MFE -25.58
Energy contribution -26.03
Covariance contribution 0.45
Combinations/Pair 1.29
Mean z-score -1.55
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.899394
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14601331 139 - 21146708
GCUGCCUAUCACUCGACACAGCUGCAAAUGUACAAAGUGCUACAUUGCAGCGAAAUCCACGAUGCAGGUGCAGUGUCAACUGAAGUUGCAUUUGCAUCAC-UAUUCGCCGAAUGCUUUUCUCCGUGGGGGGGAGGGGGUG
(((.(((....(((......(((((((.((((........)))))))))))....((((((((((((((((((..((....))..)))))))))))))..-........(((.....)))...)))))))).))).))). ( -52.40, z-score =  -2.43, R)
>droSim1.chr2R 13311425 136 - 19596830
---GCCUAUCACUCGACACAGCUGCAAAUGUACAAAGUGCUACAUUGCAGCGAAAUCCACGAUGCAGGUGCAGUGUCAACUGAAGUUGCAUUUGCAUCAC-UAUGCGCCGAAUGCUUUUCUCCGGGGGGUGGGUUGGGGG
---........((((((...(((((((.((((........))))))))))).....(((((((((((((((((..((....))..)))))))))))))..-....(.(((............))).).)))))))))).. ( -52.10, z-score =  -2.49, R)
>droSec1.super_1 12109114 124 - 14215200
---GCCUAUCACUCGACACAGCUGCAAAUGUACAAAGUGCUACAGUGCAGCGAAAUCCACGAUGCAGGUGCAGUGUCAACUGGAGUUGCAUUUGCAUCAC-UAUGCGCCGAAUGCUUUUCUACGGGGG------------
---........((((.....((((((...((((...)))).....))))))((((.....(((((((((((((..((....))..)))))))))))))..-...(((.....))).))))..))))..------------ ( -40.10, z-score =  -0.86, R)
>droYak2.chr2R 6540709 131 + 21139217
---GCCUAUCACUCGACACAGCUGCAAAUGUACAAAGUGCCACAUUGCAGCGAAAUUCUUGCUGCAGGUGCAGUGUCAACUGAAGUUGCAUUUGCAACGCUUUUUCCCCGAAUGCUUCACUCGGCGGGGGAGGG------
---.....(((...(((((.(.(((....))))...(..((....((((((((.....))))))))))..).)))))...))).(((((....))))).((((..((((((.((...)).)))).))..)))).------ ( -46.60, z-score =  -1.85, R)
>droEre2.scaffold_4845 8792556 129 - 22589142
---GCCUAUCACUCGACACAGCUGCAAGUGCACAAAGUGCUACAUUGCAGCGAAAUCCUUGCUGCAGGUGCAGUGUCAACUGGAGUUGCAUUUGCAUCAC-UUCUCCCCGAACGCUUCUCCUGGCGGAGGGGG-------
---...........(((...((((((.((((((...)))).)).(((((((((.....))))))))).)))))))))....((((((((....)))..))-))).((((...((((......))))..)))).------- ( -48.00, z-score =  -1.79, R)
>droAna3.scaffold_13266 2108002 117 + 19884421
---GCCUAUCAGUUGCCACUGCCGCAAUUCUAGUA--UUCUUUUUCCUUUUGGCAUCUGUG--GCAGAGGCAGAGGCAGUUGCAUUUGCAUUGGCUACCCCUUGGAUGCAGGCCCCUGUUUUUG----------------
---(((((((..(((((.((((((((((.((((..--............)))).)).))))--)))).))))).(((...(((....)))...)))........)))..))))...........---------------- ( -34.64, z-score =   0.11, R)
>consensus
___GCCUAUCACUCGACACAGCUGCAAAUGUACAAAGUGCUACAUUGCAGCGAAAUCCACGAUGCAGGUGCAGUGUCAACUGAAGUUGCAUUUGCAUCAC_UAUGCGCCGAAUGCUUUUCUCCGCGGGGGGGG_______
............(((.....(((((((..((((...))))....))))))).........(.(((((((((((..((....))..))))))))))).)..........)))............................. (-25.58 = -26.03 +   0.45)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:32:42 2011