Locus 5005

Sequence ID dm3.chr2R
Location 17,070,182 – 17,070,258
Length 76
Max. P 0.826085
window6874 window6875

overview

Window 4

Location 17,070,182 – 17,070,258
Length 76
Sequences 14
Columns 91
Reading direction forward
Mean pairwise identity 84.69
Shannon entropy 0.32115
G+C content 0.57417
Mean single sequence MFE -22.54
Consensus MFE -19.83
Energy contribution -19.66
Covariance contribution -0.17
Combinations/Pair 1.30
Mean z-score -1.19
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.826085
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17070182 76 + 21146708
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCUACU
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -23.70, z-score =  -1.42, R)
>droSim1.chr2R 15719075 76 + 19596830
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCUACU
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -23.70, z-score =  -1.42, R)
>droSec1.super_9 396605 76 + 3197100
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCUAUU
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -23.70, z-score =  -1.44, R)
>droYak2.chr2R 9013002 76 - 21139217
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCAACU
---------------((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))))... ( -24.90, z-score =  -1.70, R)
>droEre2.scaffold_4845 11212824 76 + 22589142
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCAACU
---------------((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))))... ( -24.90, z-score =  -1.70, R)
>dp4.chr3 17721550 76 + 19779522
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCUUGC
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -22.20, z-score =  -1.07, R)
>droPer1.super_31 862635 76 - 935084
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCUUGC
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -22.20, z-score =  -1.07, R)
>droAna3.scaffold_13266 12989830 76 - 19884421
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUCCAGU
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -23.30, z-score =  -0.65, R)
>droWil1.scaffold_180700 4811158 73 + 6630534
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCU---
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).--- ( -22.20, z-score =  -1.46, R)
>droVir3.scaffold_12875 9724045 72 - 20611582
---------------UGACCCCGACGUGAAUCGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUC----
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))---- ( -21.00, z-score =  -0.77, R)
>droMoj3.scaffold_6496 16050184 72 + 26866924
---------------UGACCCCGACGUGAAUCGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUC----
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))---- ( -21.00, z-score =  -0.77, R)
>droGri2.scaffold_15245 14334219 74 - 18325388
---------------UGACCCCGACGUGAAUCGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCCU--
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))..-- ( -21.80, z-score =  -1.13, R)
>anoGam1.chr2R 57345791 76 + 62725911
---------------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCUUCU
---------------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... ( -22.20, z-score =  -1.25, R)
>apiMel3.Group2 7681465 88 - 14465785
UGGCCUCGUAAUUCGUGACAAU-ACAUAUUUUAGAUUCUAUACUAUGCGAUUCUGACUGAAAAGUGUUCGCGUCGCGAUACAUCAUACC--
.......(((..(((((((...-........(((........))).((((.....(((....)))..))))))))))))))........-- ( -18.70, z-score =  -0.86, R)
>consensus
_______________UGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCUA_U
................(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))).... (-19.83 = -19.66 +  -0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 17,070,182 – 17,070,258
Length 76
Sequences 14
Columns 91
Reading direction reverse
Mean pairwise identity 84.69
Shannon entropy 0.32115
G+C content 0.57417
Mean single sequence MFE -26.60
Consensus MFE -24.03
Energy contribution -23.59
Covariance contribution -0.44
Combinations/Pair 1.38
Mean z-score -1.03
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17070182 76 - 21146708
AGUAGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -28.10, z-score =  -1.30, R)
>droSim1.chr2R 15719075 76 - 19596830
AGUAGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -28.10, z-score =  -1.30, R)
>droSec1.super_9 396605 76 - 3197100
AAUAGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -28.10, z-score =  -1.52, R)
>droYak2.chr2R 9013002 76 + 21139217
AGUUGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
...((((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))))--------------- ( -28.00, z-score =  -1.01, R)
>droEre2.scaffold_4845 11212824 76 - 22589142
AGUUGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
...((((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))))--------------- ( -28.00, z-score =  -1.01, R)
>dp4.chr3 17721550 76 - 19779522
GCAAGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.60, z-score =  -1.20, R)
>droPer1.super_31 862635 76 + 935084
GCAAGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.60, z-score =  -1.20, R)
>droAna3.scaffold_13266 12989830 76 + 19884421
ACUGGACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
...((((......((((.......))))))))((((((.((((....))))(((((.......))))).)))))).--------------- ( -29.80, z-score =  -1.24, R)
>droWil1.scaffold_180700 4811158 73 - 6630534
---AGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
---.(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.60, z-score =  -1.47, R)
>droVir3.scaffold_12875 9724045 72 + 20611582
----GACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAUUCACGUCGGGGUCA---------------
----(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.40, z-score =  -0.82, R)
>droMoj3.scaffold_6496 16050184 72 - 26866924
----GACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAUUCACGUCGGGGUCA---------------
----(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.40, z-score =  -0.82, R)
>droGri2.scaffold_15245 14334219 74 + 18325388
--AGGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAUUCACGUCGGGGUCA---------------
--..(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.40, z-score =  -0.60, R)
>anoGam1.chr2R 57345791 76 - 62725911
AGAAGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA---------------
....(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).--------------- ( -26.60, z-score =  -1.24, R)
>apiMel3.Group2 7681465 88 + 14465785
--GGUAUGAUGUAUCGCGACGCGAACACUUUUCAGUCAGAAUCGCAUAGUAUAGAAUCUAAAAUAUGU-AUUGUCACGAAUUACGAGGCCA
--(((....(((((((.(((((((......(((.....)))))))..((((((............)))-)))))).)))..))))..))). ( -16.70, z-score =   0.38, R)
>consensus
A_UAGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA_______________
....(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))................ (-24.03 = -23.59 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:40:05 2011