Locus 3601

Sequence ID dm3.chr2R
Location 6,636,171 – 6,636,267
Length 96
Max. P 0.947737
window4941 window4942

overview

Window 1

Location 6,636,171 – 6,636,267
Length 96
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 80.09
Shannon entropy 0.34823
G+C content 0.60271
Mean single sequence MFE -39.88
Consensus MFE -27.40
Energy contribution -28.65
Covariance contribution 1.25
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947737
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6636171 96 + 21146708
UGCCAGCGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCCGCCCGGAU--GGCUUUUAGCCAGAAUGCCUGGCCGAACCGGGCCAUUCGC---------------
.....((((.....(((((((.....)))))))..........((((((((.....--))).((..(((((.....)))))..))..)))))..))))--------------- ( -41.50, z-score =  -2.28, R)
>droAna3.scaffold_13266 18126966 111 + 19884421
GGCCAGCGACCACAUGCCACUCGUUUAGUGGCCAAAGCAGUUGUCCUGCCUCUGGCCAGGCUGUUAUCCUG--UUCCUGUACCAGUCUGCCUGUCUGCCAGUCUGGCAUUUGC
((((((.(.......((((((.....))))))....((((.....))))).))))))((((((.(((....--.....))).)))))).......((((.....))))..... ( -36.20, z-score =  -0.65, R)
>droEre2.scaffold_4845 3447478 96 - 22589142
UGCCAGCGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCUGCCCGGAU--GGCCUUUAGCCAGAAUGCCCGGCACGACCCGGCCAUUUGC---------------
.(((.(((....).(((((((.....)))))))...))....((((.((((.((.(--(((.....)))).....)).)))).).)))))).......--------------- ( -38.10, z-score =  -1.73, R)
>droYak2.chr2R 18617030 95 - 21139217
UGCCAGUGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCUGCCCGGAU--GGCUUUUACCCAGAAUGCCUGGC-CAACCCGGCCAUUCGC---------------
.....((((.....(((((((.....)))))))...(((((((((...(((.....--))).....))))).)))).((((-(.....))))).))))--------------- ( -36.50, z-score =  -1.64, R)
>droSec1.super_1 4216502 95 + 14215200
UGCCAGCGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCCGCCCGGAU--GGCUUUUAGCCAGAAUGGCUGGC-CGAACCGGCCAUUCGC---------------
.....((.......(((((((.....)))))))((((((((((((....)))))))--.)))))..))..((((((((((.-....))))))))))..--------------- ( -45.20, z-score =  -3.49, R)
>droSim1.chr2R 5242988 95 + 19596830
UGCCAGCGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCCGCCCGGAU--GGCUUUUAGCCAGAAUGCCUGGC-CGAACCGGCCAUUCGC---------------
.....((((.....(((((((.....)))))))...(((((((((....)))...(--(((.....)))))))))).((((-((...)))))).))))--------------- ( -41.80, z-score =  -2.91, R)
>consensus
UGCCAGCGACCACAGGCCACUCAUUAAGUGGCCAAAGCAUUUGGGCCCGCCCGGAU__GGCUUUUAGCCAGAAUGCCUGGC_CAACCCGGCCAUUCGC_______________
.(((.((.......(((((((.....)))))))...))(((((((....)))))))..))).........(((((.((((......)))).)))))................. (-27.40 = -28.65 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,636,171 – 6,636,267
Length 96
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.09
Shannon entropy 0.34823
G+C content 0.60271
Mean single sequence MFE -45.65
Consensus MFE -28.46
Energy contribution -29.13
Covariance contribution 0.67
Combinations/Pair 1.24
Mean z-score -2.15
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902279
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6636171 96 - 21146708
---------------GCGAAUGGCCCGGUUCGGCCAGGCAUUCUGGCUAAAAGCC--AUCCGGGCGGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCGCUGGCA
---------------((((..(((((.....((((((.....))))))....(((--.....)))))))).....((...((((((((...)))))))).))..))))..... ( -43.40, z-score =  -1.19, R)
>droAna3.scaffold_13266 18126966 111 - 19884421
GCAAAUGCCAGACUGGCAGACAGGCAGACUGGUACAGGAA--CAGGAUAACAGCCUGGCCAGAGGCAGGACAACUGCUUUGGCCACUAAACGAGUGGCAUGUGGUCGCUGGCC
((...((((((.(((.(.....).))).))))))......--((((((.((((((.((((((((.(((.....)))))))))))(((.....)))))).))).))).))))). ( -45.70, z-score =  -2.81, R)
>droEre2.scaffold_4845 3447478 96 + 22589142
---------------GCAAAUGGCCGGGUCGUGCCGGGCAUUCUGGCUAAAGGCC--AUCCGGGCAGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCGCUGGCA
---------------((...((((((((((.((((.((.....((((.....)))--).)).)))))))))....((...((((((((...)))))))).)))))))...)). ( -47.10, z-score =  -2.12, R)
>droYak2.chr2R 18617030 95 + 21139217
---------------GCGAAUGGCCGGGUUG-GCCAGGCAUUCUGGGUAAAAGCC--AUCCGGGCAGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCACUGGCA
---------------.......(((((..((-((((((((((.(((((....(((--.....)))..)))))))))))..((((((((...))))))))..))))))))))). ( -46.40, z-score =  -2.54, R)
>droSec1.super_1 4216502 95 - 14215200
---------------GCGAAUGGCCGGUUCG-GCCAGCCAUUCUGGCUAAAAGCC--AUCCGGGCGGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCGCUGGCA
---------------.......((((((..(-(((.(((....((((.....)))--)....))).)))).....(((..((((((((...))))))))...))).)))))). ( -44.40, z-score =  -1.77, R)
>droSim1.chr2R 5242988 95 - 19596830
---------------GCGAAUGGCCGGUUCG-GCCAGGCAUUCUGGCUAAAAGCC--AUCCGGGCGGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCGCUGGCA
---------------.......(((((..((-((((((((((..((((....(((--.....))).))))..))))))..((((((((...))))))))..))))))))))). ( -46.90, z-score =  -2.46, R)
>consensus
_______________GCGAAUGGCCGGGUCG_GCCAGGCAUUCUGGCUAAAAGCC__AUCCGGGCGGGCCCAAAUGCUUUGGCCACUUAAUGAGUGGCCUGUGGUCGCUGGCA
...............((.(.((((((......(((((.....)))))..(((((.......(((....)))....)))))(((((((.....)))))))..)))))).).)). (-28.46 = -29.13 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:16 2011