Locus 3835

Sequence ID dm3.chr2R
Location 8,225,243 – 8,225,353
Length 110
Max. P 0.956099
window5258 window5259

overview

Window 8

Location 8,225,243 – 8,225,353
Length 110
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 78.44
Shannon entropy 0.37174
G+C content 0.47586
Mean single sequence MFE -30.76
Consensus MFE -20.24
Energy contribution -22.72
Covariance contribution 2.48
Combinations/Pair 1.08
Mean z-score -1.34
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.536405
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8225243 110 + 21146708
AUAACUUUGCCACAUUAGGCAACACUGCAUUUCACAGUCUGCACUGCCACCUAUUUAGCGAGCAGUCUGGCAGCCCAAGCCAGAAAGUAAGAUAU---------ACAGUACGGCGACUU
......(((((......(....)((((.((.((.....((((..(((..........))).))))((((((.......))))))......)).))---------.))))..)))))... ( -27.30, z-score =  -0.84, R)
>droEre2.scaffold_4845 5022120 118 - 22589142
GUAAAUUUGCCUCAUUAGGCAACACUGUAUUUUGCACUCAGCAUUGCCAGACAUUUAGUGAGCGAUGUGGCAGCCCAGGCCUGAAAGCGAGAGAACCAAAGAGUAGAGUACAGCGACU-
......((((((....))))))(.(((((((((((..((((...((((..(((((........)))))))))((....))))))...(....).........))))))))))).)...- ( -32.70, z-score =  -1.27, R)
>droYak2.chr2R 12414311 111 - 21139217
GUAAAUUUGCCUCAUUAGGCAACACUGUAUUUUACAGUCAGCGCUGCCAAACAUUUAGCGAGCGGUGUGGCAACUCAAACUCGAAAACGAGAAGC-------AGAGAAUUCGGCGACU-
......(((((......(....).((((........((((.(((((((...........).))))))))))........((((....))))..))-------)).......)))))..- ( -27.50, z-score =  -0.35, R)
>droSec1.super_1 5771041 108 + 14215200
AUAACAUUCCCACAUUAGGCAACACUGGAUUUGACAGUCAGCGUUGCCAGACAUUUAGGGAGCAGUCUGGCAGCCUAAGCCAGAAAGCGUGAUA-----------GAGUACGGCGACUU
.......((((......((((((.((((.........)))).))))))..((.((((....((..((((((.......))))))..))....))-----------))))..)).))... ( -31.60, z-score =  -1.77, R)
>droSim1.chr2R 6693854 110 + 19596830
AUAACAUUGCCACAUUAGGCAACACUGGAUUUGACAGUCAGCGUUGCCAGACAUUUAGGGAGCAGUCUGGCAGCCUAAGCCAGAAAGCGUGAUAU---------AGAGUACGGCGACUU
......(((((......((((((.((((.........)))).))))))..((.((((....((..((((((.......))))))..))......)---------)))))..)))))... ( -34.70, z-score =  -2.48, R)
>consensus
AUAACUUUGCCACAUUAGGCAACACUGGAUUUGACAGUCAGCGUUGCCAGACAUUUAGCGAGCAGUCUGGCAGCCCAAGCCAGAAAGCGAGAUAU_________AGAGUACGGCGACUU
......(((((......((((((.(((.((......))))).)))))).............((..((((((.......))))))..)).......................)))))... (-20.24 = -22.72 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,225,243 – 8,225,353
Length 110
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 78.44
Shannon entropy 0.37174
G+C content 0.47586
Mean single sequence MFE -34.44
Consensus MFE -24.84
Energy contribution -25.48
Covariance contribution 0.64
Combinations/Pair 1.24
Mean z-score -1.97
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956099
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8225243 110 - 21146708
AAGUCGCCGUACUGU---------AUAUCUUACUUUCUGGCUUGGGCUGCCAGACUGCUCGCUAAAUAGGUGGCAGUGCAGACUGUGAAAUGCAGUGUUGCCUAAUGUGGCAAAGUUAU
.((((((((....((---------(.....)))....)))).(((....)))))))....((((..((((..(((.((((..........)))).)))..))))...))))........ ( -36.20, z-score =  -1.15, R)
>droEre2.scaffold_4845 5022120 118 + 22589142
-AGUCGCUGUACUCUACUCUUUGGUUCUCUCGCUUUCAGGCCUGGGCUGCCACAUCGCUCACUAAAUGUCUGGCAAUGCUGAGUGCAAAAUACAGUGUUGCCUAAUGAGGCAAAUUUAC
-...(((((((...(((((..((((.(((..(((....)))..)))..))))(((.(((.((.....))..))).)))..))))).....)))))))((((((....))))))...... ( -32.10, z-score =  -0.79, R)
>droYak2.chr2R 12414311 111 + 21139217
-AGUCGCCGAAUUCUCU-------GCUUCUCGUUUUCGAGUUUGAGUUGCCACACCGCUCGCUAAAUGUUUGGCAGCGCUGACUGUAAAAUACAGUGUUGCCUAAUGAGGCAAAUUUAC
-.((.(((((((.....-------((..((((....))))...((((.(.....).)))))).....))))))).))....((((((...)))))).((((((....))))))...... ( -31.70, z-score =  -1.52, R)
>droSec1.super_1 5771041 108 - 14215200
AAGUCGCCGUACUC-----------UAUCACGCUUUCUGGCUUAGGCUGCCAGACUGCUCCCUAAAUGUCUGGCAACGCUGACUGUCAAAUCCAGUGUUGCCUAAUGUGGGAAUGUUAU
..............-----------......((..((((((.......))))))..))((((...((((..((((((((((...........))))))))))..))))))))....... ( -35.80, z-score =  -3.01, R)
>droSim1.chr2R 6693854 110 - 19596830
AAGUCGCCGUACUCU---------AUAUCACGCUUUCUGGCUUAGGCUGCCAGACUGCUCCCUAAAUGUCUGGCAACGCUGACUGUCAAAUCCAGUGUUGCCUAAUGUGGCAAUGUUAU
.....(((.......---------.......((..((((((.......))))))..)).......((((..((((((((((...........))))))))))..)))))))........ ( -36.40, z-score =  -3.36, R)
>consensus
AAGUCGCCGUACUCU_________AUAUCUCGCUUUCUGGCUUGGGCUGCCAGACUGCUCCCUAAAUGUCUGGCAACGCUGACUGUAAAAUACAGUGUUGCCUAAUGUGGCAAAGUUAU
.....(((.......................((..((((((.......))))))..)).............((((((((((...........))))))))))......)))........ (-24.84 = -25.48 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:17:42 2011