Locus 2462

Sequence ID dm3.chr2L
Location 19,252,465 – 19,252,567
Length 102
Max. P 0.984485
window3385 window3386

overview

Window 5

Location 19,252,465 – 19,252,567
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.18
Shannon entropy 0.42899
G+C content 0.35782
Mean single sequence MFE -29.52
Consensus MFE -15.68
Energy contribution -15.48
Covariance contribution -0.20
Combinations/Pair 1.26
Mean z-score -2.63
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984485
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19252465 102 + 23011544
UUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUUAAUGGGGUCUAUUGAUUUCAUGGUGAGCACGGUGAUUAAU-UAUUAUCCGU---UAUGCAGAAUUUAUUCAA--------------
..((((((.......((.(((....(((.((((((((((...))))))))))))).))).))((((((((....-.)))).))))---...)))))).........-------------- ( -26.10, z-score =  -1.93, R)
>droEre2.scaffold_4845 17559820 114 - 22589142
UUUUCUGCUGUUUUUGCACGCAGAAAUGGAAACCAAUGGGGUCUAUUGAUUUCAUGGCGAGCAUUGUGAUUAAUACAUUUCACA----CAUUAAUAAUCUGCUAUAAUAAUGGGUUCA--
.((((((((((....))).)))))))......(((.((..(((....)))..))))).((((..(((((..........)))))----(((((.((........)).))))).)))).-- ( -29.30, z-score =  -2.34, R)
>droYak2.chr2R 5760042 120 + 21139217
UUUUCUGCUGUUUUUGUACGCAGAAAUGGCAAUGACUCGGGUCUAUUGAUUUCAUGGUGUGCAUGGCGAUUUUCACAUUACAUAUGUACAUUAAUAACCCGCUAUUAUGGUUUUUUUUUA
.....(((((((((((....)))))))))))((((..(((((.(((((((..((((.((((.(((..........)))))))))))...))))))))))))...))))............ ( -28.80, z-score =  -1.91, R)
>droSec1.super_7 2875812 102 + 3727775
UUUUCUGCUGUUUUUGCACGCUGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCGUGGUGAGCAUGGUGAUUAAU-UAUUAUUCGC---UAUGCAGGAUUUAUUCAA--------------
..((((((.(((((..(.(((....)))(((((((((((...))))))))))))..).))))(((((((.((..-...)).))))---))))))))).........-------------- ( -29.90, z-score =  -2.88, R)
>droSim1.chr2L 18942568 102 + 22036055
UUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUGAUUAAU-UAUUAUUCGC---UAUGCAGGAUUUAUUCAA--------------
.((((((((((....))).)))))))..(((((((((((...))))))))))).......(((((((((.((..-...)).))))---))))).............-------------- ( -33.50, z-score =  -4.12, R)
>consensus
UUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUGAUUAAU_UAUUAUACGC___UAUGCAGAAUUUAUUCAA______________
..(((((((((....))).))))))(((...((((.(((((((....)))))))))))...)))........................................................ (-15.68 = -15.48 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,252,465 – 19,252,567
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.18
Shannon entropy 0.42899
G+C content 0.35782
Mean single sequence MFE -19.16
Consensus MFE -10.42
Energy contribution -11.26
Covariance contribution 0.84
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874928
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19252465 102 - 23011544
--------------UUGAAUAAAUUCUGCAUA---ACGGAUAAUA-AUUAAUCACCGUGCUCACCAUGAAAUCAAUAGACCCCAUUAAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAA
--------------.........((((((...---((((......-........))))((.......(((((.(((.......))).))))).......))...........)))))).. ( -14.38, z-score =  -0.95, R)
>droEre2.scaffold_4845 17559820 114 + 22589142
--UGAACCCAUUAUUAUAGCAGAUUAUUAAUG----UGUGAAAUGUAUUAAUCACAAUGCUCGCCAUGAAAUCAAUAGACCCCAUUGGUUUCCAUUUCUGCGUGCAAAAACAGCAGAAAA
--...............((((....(((((((----..(...)..))))))).....))))......(((((((((.......)))))))))..(((((((((......)).))))))). ( -22.00, z-score =  -1.31, R)
>droYak2.chr2R 5760042 120 - 21139217
UAAAAAAAAACCAUAAUAGCGGGUUAUUAAUGUACAUAUGUAAUGUGAAAAUCGCCAUGCACACCAUGAAAUCAAUAGACCCGAGUCAUUGCCAUUUCUGCGUACAAAAACAGCAGAAAA
...................((((((.......(((((.....)))))........((((.....)))).........))))))...........(((((((((......)).))))))). ( -21.60, z-score =  -1.29, R)
>droSec1.super_7 2875812 102 - 3727775
--------------UUGAAUAAAUCCUGCAUA---GCGAAUAAUA-AUUAAUCACCAUGCUCACCACGAAAUCAAUAGACCCCAUUGAUUUCCACUUCAGCGUGCAAAAACAGCAGAAAA
--------------...........((((...---..((.((...-..)).))..((((((......(((((((((.......)))))))))......))))))........)))).... ( -18.90, z-score =  -3.32, R)
>droSim1.chr2L 18942568 102 - 22036055
--------------UUGAAUAAAUCCUGCAUA---GCGAAUAAUA-AUUAAUCACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAA
--------------.............((((.---(.((.((...-..)).)).).)))).......(((((((((.......)))))))))...((((((((......)).)))))).. ( -18.90, z-score =  -2.91, R)
>consensus
______________UUGAAUAAAUUCUGCAUA___ACGAAUAAUA_AUUAAUCACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAA
...................................................................(((((((((.......)))))))))...((((((((......)).)))))).. (-10.42 = -11.26 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:39 2011