Locus 12154

Sequence ID dm3.chr3R
Location 26,073,655 – 26,073,716
Length 61
Max. P 0.945753
window16714 window16715

overview

Window 4

Location 26,073,655 – 26,073,716
Length 61
Sequences 11
Columns 66
Reading direction forward
Mean pairwise identity 71.20
Shannon entropy 0.61911
G+C content 0.44138
Mean single sequence MFE -10.75
Consensus MFE -8.48
Energy contribution -8.57
Covariance contribution 0.09
Combinations/Pair 1.00
Mean z-score -0.55
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927292
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26073655 61 + 27905053
-UUAAAUGAGGAAAAAAAAGUAAUAUUAACC----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-......((((........((..........----..)).(((.((((.......))))))))))) ( -10.30, z-score =  -0.38, R)
>droAna3.scaffold_13340 21114509 60 + 23697760
-CUUAACAAAAAAUGUAAGGAUAAACCCAC-----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-...............((((.....(((((-----((....)))))))...((......)).)))) ( -13.10, z-score =  -1.29, R)
>droEre2.scaffold_4820 8547562 60 - 10470090
-UUCAAUUAUCUAAAAAAAAGAAUUCAACU-----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-.............................-----.....(((.((((.......))))))).... (  -9.10, z-score =  -0.35, R)
>droYak2.chr3R 27007523 58 + 28832112
-UUAAAUGAGGAAAAAAA--GAAU-UCAACA----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-......((((.......--....-((....----.))..(((.((((.......))))))))))) ( -11.10, z-score =  -0.80, R)
>droSec1.super_4 4924047 61 + 6179234
-UUAAAUGAGAAAAAAAAAAGAAUAUUAACU----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-..............................----.....(((.((((.......))))))).... (  -9.10, z-score =  -0.80, R)
>droSim1.chr3R 25739734 61 + 27517382
-UUAAAUGAGGAAAAAAAAAGAAUAUUAACC----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-......((((........((.........)----)....(((.((((.......))))))))))) ( -10.00, z-score =  -0.49, R)
>droPer1.super_7 210799 61 - 4445127
-UUGCUCGAAGCAAAAAAUCUCUUUCGUUUC----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-.((((.(((((.(((......))).)))))----....))))(((((.......)))))...... ( -13.40, z-score =  -0.28, R)
>dp4.chr2 29359969 61 - 30794189
-UUGCUCGAAGCAAAAAAUCUCUUUCGUUUC----UGACAGCGGUGGGAUUCGAACCCACGCCCUU
-.((((.(((((.(((......))).)))))----....))))(((((.......)))))...... ( -13.40, z-score =  -0.28, R)
>droVir3.scaffold_12855 3168654 66 + 10161210
CCACCAGGAAAAAAAAAAUAGAAAGCAUCUCAACUUGACAGCGGUGGGAUUCGAACCCACGCCCUU
.....(((................((.((.......))..)).(((((.......)))))..))). ( -10.80, z-score =   0.05, R)
>droGri2.scaffold_14906 5858775 54 + 14172833
---CCACCAAAAAUAAACUUGUAAAC---------UGACAGCGGUGGGAUUCGAACCCACGCCCUU
---.......................---------.....(((.((((.......))))))).... (  -9.10, z-score =  -0.34, R)
>anoGam1.chr2R 37002181 54 - 62725911
--UCAUAUCAACAAAAAAGCUCAUUUGU----------CAGAAGUGGGAUUCGAACCCACGCCUAC
--.....((.(((((........)))))----------..)).(((((.......)))))...... (  -8.90, z-score =  -1.10, R)
>consensus
_UUAAAUGAAAAAAAAAAAAGAAUACGAACC____UGACAGCGGUGGGAUUCGAACCCACGCCCUU
........................................((.(((((.......))))))).... ( -8.48 =  -8.57 +   0.09)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 26,073,655 – 26,073,716
Length 61
Sequences 11
Columns 66
Reading direction reverse
Mean pairwise identity 71.20
Shannon entropy 0.61911
G+C content 0.44138
Mean single sequence MFE -13.52
Consensus MFE -10.58
Energy contribution -10.59
Covariance contribution 0.01
Combinations/Pair 1.12
Mean z-score -0.67
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945753
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26073655 61 - 27905053
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----GGUUAAUAUUACUUUUUUUUCCUCAUUUAA-
...((((((((.......)))).))))...(----((..((..........))..))).......- ( -11.70, z-score =  -0.52, R)
>droAna3.scaffold_13340 21114509 60 - 23697760
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA-----GUGGGUUUAUCCUUACAUUUUUUGUUAAG-
...((((((((.......)))).))))....-----(((((......))))).............- ( -14.50, z-score =  -0.76, R)
>droEre2.scaffold_4820 8547562 60 + 10470090
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA-----AGUUGAAUUCUUUUUUUUAGAUAAUUGAA-
...((((((((.......)))).)))).(((-----(.(((((........)))))....)))).- ( -13.90, z-score =  -0.89, R)
>droYak2.chr3R 27007523 58 - 28832112
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----UGUUGA-AUUC--UUUUUUUCCUCAUUUAA-
...((((((((.......)))).))))...(----((..((-(...--.....)))..)))....- ( -12.90, z-score =  -1.03, R)
>droSec1.super_4 4924047 61 - 6179234
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----AGUUAAUAUUCUUUUUUUUUUCUCAUUUAA-
...((((((((.......)))).))))....----..............................- ( -11.20, z-score =  -1.21, R)
>droSim1.chr3R 25739734 61 - 27517382
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----GGUUAAUAUUCUUUUUUUUUCCUCAUUUAA-
...((((((((.......)))).))))...(----((..((..........))..))).......- ( -11.70, z-score =  -0.65, R)
>droPer1.super_7 210799 61 + 4445127
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----GAAACGAAAGAGAUUUUUUGCUUCGAGCAA-
...((((((((.......)))).))))((..----(((.((((((....)))))).)))..))..- ( -16.80, z-score =  -0.56, R)
>dp4.chr2 29359969 61 + 30794189
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----GAAACGAAAGAGAUUUUUUGCUUCGAGCAA-
...((((((((.......)))).))))((..----(((.((((((....)))))).)))..))..- ( -16.80, z-score =  -0.56, R)
>droVir3.scaffold_12855 3168654 66 - 10161210
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCAAGUUGAGAUGCUUUCUAUUUUUUUUUUCCUGGUGG
.((((((((((.......)))).)))....((((......))))..............)))..... ( -13.20, z-score =   0.69, R)
>droGri2.scaffold_14906 5858775 54 - 14172833
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA---------GUUUACAAGUUUAUUUUUGGUGG---
...((((((((.......)))).))))....---------.....((((......))))....--- ( -12.30, z-score =  -0.36, R)
>anoGam1.chr2R 37002181 54 + 62725911
GUAGGCGUGGGUUCGAAUCCCACUUCUG----------ACAAAUGAGCUUUUUUGUUGAUAUGA--
.((((.(((((.......))))).))))----------.((.((.(((......))).)).)).-- ( -13.70, z-score =  -1.50, R)
>consensus
AAGGGCGUGGGUUCGAAUCCCACCGCUGUCA____GGUUAGUAUUCUAUUUUUUUCUUCAUUGAA_
...((((((((.......)))).))))....................................... (-10.58 = -10.59 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:56:49 2011