Locus 3356

Sequence ID dm3.chr2R
Location 4,607,000 – 4,607,126
Length 126
Max. P 0.896379
window4616 window4617

overview

Window 6

Location 4,607,000 – 4,607,126
Length 126
Sequences 5
Columns 138
Reading direction forward
Mean pairwise identity 75.84
Shannon entropy 0.41569
G+C content 0.37808
Mean single sequence MFE -32.78
Consensus MFE -16.33
Energy contribution -16.82
Covariance contribution 0.49
Combinations/Pair 1.16
Mean z-score -2.13
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.846793
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4607000 126 + 21146708
UAACGAACAAUGCAUAAGUACAUUAAUCUC------------CCUAUUAAAAGAGUCCUAGAAACCUCGAAGGAUUUAAGAAGGCUAUUUAAGCUUUACUAAAGUAAAGUGGCGAUUUAAAUCUUUUGAGGUCUCUGU
....((..((((........))))..))..------------................((((.(((((((((((((((((...(((......(((((((....))))))))))..))))))))))))))))).)))). ( -32.20, z-score =  -2.90, R)
>droEre2.scaffold_4929 8606363 132 - 26641161
UAACCAAGCAUGCACAUGUACAUUAAUCUUGAAGAAUAAGAACCUUAUAAGGAAGUCCAAGAAACCGCUAGGGAUUUAAGAAAGCUACUUUCGUUU-GCCGAAGUA-----GCGGUUUAAAUCUGUUGCGGUCUUUGU
...((..((((....)))).......(((((.....))))).........)).......(((.(((((.(.(((((((((...((((((((.(...-.).))))))-----))..))))))))).).))))).))).. ( -34.70, z-score =  -2.14, R)
>droYak2.chr2L 17270634 132 + 22324452
CAAUCAACAAUGCAUUAGUACAUUAAGCUUAAAGAGUAUGAACCUUUUAAGGAAUUCCCAGAAACCUCUACGGAUUUAAGAAGGCUAAUUUGGCUGAA-UGAAGUA-----GCGGUUUAAAUCUGUUGAGCUCUCUGA
...((...((((........))))...(((((((.((....)).))))))))).....((((...(((.(((((((((((...((((.((((......-)))).))-----))..))))))))))).)))...)))). ( -27.50, z-score =  -0.15, R)
>droSec1.super_1 2251441 113 + 14215200
AAACGAACAAUGCAUAAGUAUAUUAAUCUC------------CCUUCUAAGGGAGUCCCAGAAACCUCUAGUGAUUUCAGAAGGCUAUUUUCGC--------GGUA-----GCGGUUUAAAUCUGUUGAGGUCUCUGU
.........((((....))))......(((------------(((....))))))...((((.(((((....(((((.(((..((((((.....--------))))-----))..))))))))....))))).)))). ( -31.90, z-score =  -2.28, R)
>droSim1.chr2R 3290807 120 + 19596830
AAACGAACAAUGCAUAAGUACAU-AAUCUC------------CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUUUACAGAAGUA-----GCGGUUUAAAUCUGUUGAGGUCUCUGU
.......................-...(((------------(((....))))))...((((.(((((.(.(((((((((...(((((((..(.....)..)))))-----))..))))))))).).))))).)))). ( -37.60, z-score =  -3.20, R)
>consensus
AAACGAACAAUGCAUAAGUACAUUAAUCUC____________CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUU_ACUGAAGUA_____GCGGUUUAAAUCUGUUGAGGUCUCUGU
..........................................................((((.(((((.(.(((((((((...((.......((((.....))))......))..))))))))).).))))).)))). (-16.33 = -16.82 +   0.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,607,000 – 4,607,126
Length 126
Sequences 5
Columns 138
Reading direction reverse
Mean pairwise identity 75.84
Shannon entropy 0.41569
G+C content 0.37808
Mean single sequence MFE -32.20
Consensus MFE -14.51
Energy contribution -15.99
Covariance contribution 1.48
Combinations/Pair 1.04
Mean z-score -2.47
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.13
SVM RNA-class probability 0.896379
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4607000 126 - 21146708
ACAGAGACCUCAAAAGAUUUAAAUCGCCACUUUACUUUAGUAAAGCUUAAAUAGCCUUCUUAAAUCCUUCGAGGUUUCUAGGACUCUUUUAAUAGG------------GAGAUUAAUGUACUUAUGCAUUGUUCGUUA
..(((((((((.((.(((((((........(((((....)))))(((.....)))....))))))).)).)))))))))....((((......)))------------).((.(((((((....))))))).)).... ( -30.80, z-score =  -2.44, R)
>droEre2.scaffold_4929 8606363 132 + 26641161
ACAAAGACCGCAACAGAUUUAAACCGC-----UACUUCGGC-AAACGAAAGUAGCUUUCUUAAAUCCCUAGCGGUUUCUUGGACUUCCUUAUAAGGUUCUUAUUCUUCAAGAUUAAUGUACAUGUGCAUGCUUGGUUA
....(((((((....(((((((...((-----(((((((..-...)).)))))))....)))))))....)))))))...((((((.......)))))).......(((((....(((((....))))).)))))... ( -35.60, z-score =  -3.15, R)
>droYak2.chr2L 17270634 132 - 22324452
UCAGAGAGCUCAACAGAUUUAAACCGC-----UACUUCA-UUCAGCCAAAUUAGCCUUCUUAAAUCCGUAGAGGUUUCUGGGAAUUCCUUAAAAGGUUCAUACUCUUUAAGCUUAAUGUACUAAUGCAUUGUUGAUUG
(((((((.(((.((.(((((((...((-----((.....-...........))))....))))))).)).))).)))))))......((((((..((....))..))))))..(((((((....)))))))....... ( -28.99, z-score =  -1.42, R)
>droSec1.super_1 2251441 113 - 14215200
ACAGAGACCUCAACAGAUUUAAACCGC-----UACC--------GCGAAAAUAGCCUUCUGAAAUCACUAGAGGUUUCUGGGACUCCCUUAGAAGG------------GAGAUUAAUAUACUUAUGCAUUGUUCGUUU
.((((((((((....(((((.....((-----((..--------.......))))......)))))....))))))))))...((((((....)))------------)))........................... ( -30.60, z-score =  -2.51, R)
>droSim1.chr2R 3290807 120 - 19596830
ACAGAGACCUCAACAGAUUUAAACCGC-----UACUUCUGUAAAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAGAAGG------------GAGAUU-AUGUACUUAUGCAUUGUUCGUUU
.((((((((((....(((((((...((-----((.((.((.....)).)).))))....)))))))....))))))))))(((((((((....)))------------)))...-(((((....)))))..))).... ( -35.00, z-score =  -2.85, R)
>consensus
ACAGAGACCUCAACAGAUUUAAACCGC_____UACUUCAGU_AAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAAAAGG____________GAGAUUAAUGUACUUAUGCAUUGUUCGUUA
.((((((((((....(((((((...((..........................))....)))))))....)))))))))).................................(((((((....)))))))....... (-14.51 = -15.99 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:08:40 2011