Locus 10493

Sequence ID	dm3.chr3R
Location	14,156,304 – 14,156,372
Length	68
Max. P	0.962398

overview

Window 4

Location	14,156,304 – 14,156,372
Length	68
Sequences	5
Columns	77
Reading direction	forward
Mean pairwise identity	68.11
Shannon entropy	0.55510
G+C content	0.52895
Mean single sequence MFE	-18.02
Consensus MFE	-10.64
Energy contribution	-12.32
Covariance contribution	1.68
Combinations/Pair	1.07
Mean z-score	-1.03
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.82
SVM RNA-class probability	0.827533
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14156304 68 + 27905053
---CUUUCACAGCCCCUAUGGG---AGCCAUGGACUAUGGAAAGUGCACUCCAUGCACUUUGCGCCUCCAGUUC---
---........(((((...)))---.))..((((...((.((((((((.....)))))))).))..))))....--- ( -20.10, z-score =  -1.18, R)
>droSim1.chr3R 20197042 74 - 27517382
UUUCAUACACAGCCCCUAUGGGAGGAGCCAUGGUCUAUGGAAAGUGCACUCCAUGCACUUUGCGCCUUCAGUUC---
....................(((((.((...(((.((((((........)))))).)))..)).))))).....--- ( -18.50, z-score =   0.07, R)
>droSec1.super_5 125973 74 - 5866729
UUUCAUACACAGCCCCUAUGGGAGGAGCCAUGGUCUAUGGAAAGUGCACUCCAUGCACUUUGCGCCUUCAGUUC---
....................(((((.((...(((.((((((........)))))).)))..)).))))).....--- ( -18.50, z-score =   0.07, R)
>droEre2.scaffold_4770 10266990 67 - 17746568
---UUUCCACAGCCCCCAUGG----AGCCCCGGACUGUGGAAAGUGCACUCCAUGCACUUUACGCCUCCAGUUC---
---(((((((((.((....((----....)))).)))))))))(((((.....)))))................--- ( -20.50, z-score =  -2.31, R)
>droAna3.scaffold_13340 13754576 59 - 23697760
------------------UCGACGAGCCCCUAUGGAAACGAAAAUGCAUCCAAUGCACUUUACGCUUCCACAUGCGU
------------------.......((.....(((((.(((((.(((((...))))).))).)).)))))...)).. ( -12.50, z-score =  -1.81, R)
>consensus
___CAUACACAGCCCCUAUGGG_G_AGCCAUGGACUAUGGAAAGUGCACUCCAUGCACUUUGCGCCUCCAGUUC___
...............((((((......)))))).....(.((((((((.....)))))))).).............. (-10.64 = -12.32 +   1.68)

alignment

secondary structure

dotplot

Window 5

Location	14,156,304 – 14,156,372
Length	68
Sequences	5
Columns	77
Reading direction	reverse
Mean pairwise identity	68.11
Shannon entropy	0.55510
G+C content	0.52895
Mean single sequence MFE	-24.80
Consensus MFE	-11.68
Energy contribution	-13.32
Covariance contribution	1.64
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.47
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.71
SVM RNA-class probability	0.962398
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14156304 68 - 27905053
---GAACUGGAGGCGCAAAGUGCAUGGAGUGCACUUUCCAUAGUCCAUGGCU---CCCAUAGGGGCUGUGAAAG---
---..((((..((...(((((((((...))))))))))).)))).(((((((---((....)))))))))....--- ( -24.30, z-score =  -1.51, R)
>droSim1.chr3R 20197042 74 + 27517382
---GAACUGAAGGCGCAAAGUGCAUGGAGUGCACUUUCCAUAGACCAUGGCUCCUCCCAUAGGGGCUGUGUAUGAAA
---........((...(((((((((...)))))))))))......((((((((((.....))))))))))....... ( -23.40, z-score =  -0.93, R)
>droSec1.super_5 125973 74 + 5866729
---GAACUGAAGGCGCAAAGUGCAUGGAGUGCACUUUCCAUAGACCAUGGCUCCUCCCAUAGGGGCUGUGUAUGAAA
---........((...(((((((((...)))))))))))......((((((((((.....))))))))))....... ( -23.40, z-score =  -0.93, R)
>droEre2.scaffold_4770 10266990 67 + 17746568
---GAACUGGAGGCGUAAAGUGCAUGGAGUGCACUUUCCACAGUCCGGGGCU----CCAUGGGGGCUGUGGAAA---
---...(((..((...(((((((((...))))))))))).)))((((.((((----((...)))))).))))..--- ( -27.70, z-score =  -2.25, R)
>droAna3.scaffold_13340 13754576 59 + 23697760
ACGCAUGUGGAAGCGUAAAGUGCAUUGGAUGCAUUUUCGUUUCCAUAGGGGCUCGUCGA------------------
..((.((((((((((.(((((((((...)))))))))))))))))))...)).......------------------ ( -25.20, z-score =  -4.29, R)
>consensus
___GAACUGGAGGCGCAAAGUGCAUGGAGUGCACUUUCCAUAGACCAUGGCU_C_CCCAUAGGGGCUGUGUAAG___
..............(.(((((((((...))))))))))(((((.((((((......))))..)).)))))....... (-11.68 = -13.32 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:25:03 2011