Locus 9416

Sequence ID dm3.chr3R
Location 6,550,871 – 6,551,062
Length 191
Max. P 0.939541
window12910 window12911 window12912

overview

Window 0

Location 6,550,871 – 6,550,962
Length 91
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 63.67
Shannon entropy 0.62823
G+C content 0.44528
Mean single sequence MFE -23.44
Consensus MFE -11.16
Energy contribution -11.70
Covariance contribution 0.54
Combinations/Pair 1.53
Mean z-score -0.79
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.546226
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6550871 91 + 27905053
-------------GGUAUA-CAUUUUGGCUUCUCUGACAGACAGCC-GCAUUAAAGGCAGGAACUUGGCCAAAAGAA----------AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
-------------(((...-..(((((((((((.....)))..(((-........)))........))))))))...----------...((((((....)))))).....))).. ( -26.20, z-score =  -1.14, R)
>droSim1.chr3R 12706735 91 - 27517382
-------------GGUAUA-CAUUUUGGCUUCUCUGACAGACAGCC-GCAUUAAAGGCAGGAACUUGGCCAAAAGAA----------AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
-------------(((...-..(((((((((((.....)))..(((-........)))........))))))))...----------...((((((....)))))).....))).. ( -26.20, z-score =  -1.14, R)
>droSec1.super_0 5729580 91 - 21120651
-------------GGUAUA-CAUGUUGGCUUCUCUGACAGACAGUC-GCAUUAAAGGCAGGAACUUGGCCAAAAGAA----------AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
-------------(((...-....((((((..((((((.....)))-((.......)).)))....)))))).....----------...((((((....)))))).....))).. ( -24.50, z-score =  -0.65, R)
>droEre2.scaffold_4770 2692993 91 - 17746568
-------------GGUACA-CAUUUUGGCUUCUUUGACAGACAGCC-GUAUUAAAGGCAGGAACUUGGCCAAAAGAA----------AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
-------------(((...-..(((((((((((.....)))..(((-........)))........))))))))...----------...((((((....)))))).....))).. ( -26.20, z-score =  -1.44, R)
>droYak2.chr3R 10589556 91 + 28832112
-------------GGUAUA-CAUUUUGGCUUCUCUGACAGACAGCC-GUAUUAAAGGCAGGAACUUGGCCAAAAGAA----------AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
-------------(((...-..(((((((((((.....)))..(((-........)))........))))))))...----------...((((((....)))))).....))).. ( -26.20, z-score =  -1.31, R)
>droWil1.scaffold_181089 7908409 82 - 12369635
-----------------------UGUUUAUGCCCUU-CACUUUAUUCGAAAGACCGAACAAAGUUUGAGUAGAACAUUUG-------CCAGUUCUCAUUGGAGUCAUUUCAAC---
-----------------------((...(((..(((-((((((.((((......)))).)))))....(.(((((.....-------...))))))...)))).)))..))..--- ( -13.90, z-score =  -0.35, R)
>droGri2.scaffold_14830 3238411 113 - 6267026
CGAUUAUGCGUUUGCCAGAACAUUACCUCCGUGUCAAUAAAUUGUUAGCAUUGCCAAUGAAAGUUCAAGUGAAACAACAAAAGCACUAAAGGACUCCUUUUGGCUCAUUUGGC---
.............((((((...........(((..(((.....)))..))).(((((....(((((.((((............))))...)))))....)))))...))))))--- ( -20.90, z-score =   0.48, R)
>consensus
_____________GGUAUA_CAUUUUGGCUUCUCUGACAGACAGCC_GCAUUAAAGGCAGGAACUUGGCCAAAAGAA__________AAAGGGCUCAUUUGGGCCCAUUCAGCUAG
......................((((((((..((((.(.................).)))).....))))))))................((((((....)))))).......... (-11.16 = -11.70 +   0.54)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,550,896 – 6,550,999
Length 103
Sequences 8
Columns 110
Reading direction forward
Mean pairwise identity 67.68
Shannon entropy 0.65101
G+C content 0.43791
Mean single sequence MFE -29.86
Consensus MFE -10.00
Energy contribution -11.01
Covariance contribution 1.02
Combinations/Pair 1.35
Mean z-score -2.17
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939541
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6550896 103 + 27905053
----GACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAGUUUAUCUG
----(((((((........))).......((((((((.......((((((....)))))).........(((........)))..)))))))))---))).......... ( -35.10, z-score =  -2.72, R)
>droSim1.chr3R 12706760 103 - 27517382
----GACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAGUUUAUCUG
----(((((((........))).......((((((((.......((((((....)))))).........(((........)))..)))))))))---))).......... ( -35.10, z-score =  -2.72, R)
>droSec1.super_0 5729605 103 - 21120651
----GACAGUCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAGUUUAUCUG
----(((((((........))).......((((((((.......((((((....)))))).........(((........)))..)))))))))---))).......... ( -32.40, z-score =  -2.15, R)
>droEre2.scaffold_4770 2693018 103 - 17746568
----GACAGCCGUAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAGUUUAUCUG
----(((((((........))).......((((((((.......((((((....)))))).........(((........)))..)))))))))---))).......... ( -35.10, z-score =  -2.90, R)
>droYak2.chr3R 10589581 103 + 28832112
----GACAGCCGUAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAGUUUAUCUG
----(((((((........))).......((((((((.......((((((....)))))).........(((........)))..)))))))))---))).......... ( -35.10, z-score =  -2.90, R)
>droAna3.scaffold_13340 1196372 84 + 23697760
-----------------------CAUUUUCUGGCGAAAGAAAAAGGGCUCAUUUGGGCUCACUCAGAUAGACAUUGACCAGUCCAUUUGGCCAU---GUCAAUUUAUCUG
-----------------------..((((((......)))))).((((((....))))))...(((((((((((.(.((((.....))))).))---)))....)))))) ( -25.30, z-score =  -2.55, R)
>droVir3.scaffold_13047 12061978 93 - 19223366
AUAAAUGUUAAGUAUUGUAAGUUGAAGUU--------------AAAGAACUAAAGGACAC-UCUUGGCC--CAUUUGGCAGUCCAUUUAGCCGUUUCAUCAAUUUAUGCG
................(((((((((.(..--------------......(((((((((.(-....)(((--.....))).)))).)))))......).)))))))))... ( -17.64, z-score =  -0.75, R)
>droGri2.scaffold_14830 3238447 108 - 6267026
AUAAAUUGUUAGCAUUGCCAAUGAAAGUUCAAGUGAAACAACAAAAGCACUAAAGGACUCCUUUUGGCU--CAUUUGGCAGGCCAUUUAGCAGUUUCAUCAAUUUAUGCG
((((((((..(((.((((((((((........((......))....((...(((((...)))))..)))--)).)))))))((......)).)))....))))))))... ( -23.10, z-score =  -0.70, R)
>consensus
____GACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAU___GUCAGUUUAUCUG
........................(((((...............((((((....)))))).........(((..((.((((.....)))).))....))))))))..... (-10.00 = -11.01 +   1.02)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,550,960 – 6,551,062
Length 102
Sequences 8
Columns 103
Reading direction reverse
Mean pairwise identity 83.70
Shannon entropy 0.31870
G+C content 0.46441
Mean single sequence MFE -30.30
Consensus MFE -18.90
Energy contribution -18.70
Covariance contribution -0.20
Combinations/Pair 1.40
Mean z-score -1.86
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.641603
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6550960 102 - 27905053
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGACCAGAUCGAUGGGGC-AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((..(((-.....(((.....))).....)))..)).)))))))))...... ( -28.50, z-score =  -1.66, R)
>droSim1.chr3R 12706824 102 + 27517382
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGGCCAGAUCGAUGGGCC-AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((.((((-(....(((.....)))...)))))..)).)))))))))...... ( -28.80, z-score =  -1.48, R)
>droSec1.super_0 5729669 102 + 21120651
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGGCCAGAUCGAUGGGGC-AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((..(((-.....(((.....))).....)))..)).)))))))))...... ( -27.90, z-score =  -1.08, R)
>droEre2.scaffold_4770 2693082 102 + 17746568
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGGCCAGAUCGAUGGGGC-AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((..(((-.....(((.....))).....)))..)).)))))))))...... ( -27.90, z-score =  -1.08, R)
>droYak2.chr3R 10589645 102 - 28832112
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGGCCAGAUCGAUGGGGC-AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((..(((-.....(((.....))).....)))..)).)))))))))...... ( -27.90, z-score =  -1.08, R)
>droAna3.scaffold_13340 1196417 103 - 23697760
GUUACGUGCCGACGACCGGCCCAUAACACUUCAGAUGUAAUGGCCAGAUCGAUGGGCCAAAACGCAGAUAAAUUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.((((.....)))).).)))).....((((((..(((((((.((.((.(((((.....(((.....)))...)))))..)).))))))))))))))) ( -32.60, z-score =  -1.91, R)
>dp4.chr2 1390882 100 + 30794189
-UUACGUGCUGAUGCCAUGGCCAUAACACUUCAAAUGUAAUGGCCAUGGCCAGAUCGAUGGACG-AGACACACUCACA-GAUAAACUCAGAUGGCCAAUGUCC
-...((..(((..(((((((((((.(((.......))).))))))))))))))..))..(((((-((.....)))...-((.....))...........)))) ( -32.50, z-score =  -3.00, R)
>droPer1.super_6 1366995 101 + 6141320
GUUACGUGCUGAUGCCAUGGCCAUAACACUUCAAAUGUAAUGGCCAUGGCCAGAUCGAUGGACG-AGACACACUCACA-GAUAAACUCACGUGGCCAAUGUCC
(((((((((((..(((((((((((.(((.......))).))))))))))))))..........(-((.....)))...-........))))))))........ ( -36.30, z-score =  -3.58, R)
>consensus
GUUACGUGCUGAUGUCCAAGCCAUAACACUUCAAAUGUAAUGGCCAGAUCGAUGGGGC_AAACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCU
((((.(.(((........)))).)))).............(((((((.((.((..(((......(((.....))).....)))..)).)))))))))...... (-18.90 = -18.70 +  -0.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:03:59 2011