Locus 4070

Sequence ID dm3.chr2R
Location 10,162,610 – 10,162,709
Length 99
Max. P 0.979101
window5578 window5579

overview

Window 8

Location 10,162,610 – 10,162,709
Length 99
Sequences 10
Columns 111
Reading direction forward
Mean pairwise identity 77.05
Shannon entropy 0.46087
G+C content 0.50990
Mean single sequence MFE -30.87
Consensus MFE -18.23
Energy contribution -18.59
Covariance contribution 0.36
Combinations/Pair 1.43
Mean z-score -2.09
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.91
SVM RNA-class probability 0.974534
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10162610 99 + 21146708
CUCACUGUAAGGACACGCUGUGCUCUGACCUUACAGCUG------AACAUGUGCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU------UUGUUUACUUGGACG
.(((((((((((.((.((...))..)).)))))))).))------)((((((((((.(((..((........)).)))))))))))))..------..((((....)))). ( -32.90, z-score =  -2.73, R)
>droAna3.scaffold_13266 14512666 105 + 19884421
CUCACUGUAAGGACACGCUGAGCUCUGACCUUACAGCUGAACAUGAACAUGUGCGCGACGUCCUAUUAUCACAGUCGUGCGCACAUGUAU------UUGUUUACUUGGACG
....((((((((.((.((...))..)).)))))))).((((((...((((((((((.(((.(...........).)))))))))))))..------.))))))........ ( -35.10, z-score =  -2.95, R)
>droEre2.scaffold_4845 6909901 99 - 22589142
CUCACUGUAAGGACACGCUGUGCUCUGACCUUACAGCUG------AACAUGUGCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU------UUGUUUACUUGGACG
.(((((((((((.((.((...))..)).)))))))).))------)((((((((((.(((..((........)).)))))))))))))..------..((((....)))). ( -32.90, z-score =  -2.73, R)
>droYak2.chr2R 10099787 99 + 21139217
CUCACUGUAAGGACACGCUGUACUCUGACCUUACAGCUG------AACAUGUUCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU------UUGUUUACUUGGACG
.(((((((((((.((..........)).)))))))).))------)((((((.(((.(((..((........)).)))))).))))))..------..((((....)))). ( -25.00, z-score =  -1.14, R)
>droSec1.super_1 7670266 99 + 14215200
CUCACUGUAAGGACACGCUGUGCUCUGACCUUACAGCUG------AACAUGUGCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU------UUGUUUACUUGGACG
.(((((((((((.((.((...))..)).)))))))).))------)((((((((((.(((..((........)).)))))))))))))..------..((((....)))). ( -32.90, z-score =  -2.73, R)
>droSim1.chr2R 8925506 99 + 19596830
CUCACUGUAAGGACACGCUGUGCUCUGACCUUACAGCUU------AACAUGUGCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU------UUGUUUACUUGGACG
....((((((((.((.((...))..)).))))))))...------.((((((((((.(((..((........)).)))))))))))))..------..((((....)))). ( -30.50, z-score =  -2.26, R)
>droMoj3.scaffold_6496 12808570 93 + 26866924
UGCACUGUAAGGACGCGCUCUGCUCUGACCUUACAGCUACAGCUGAACAUGUGCGCGCCGCGCGC------------UAUGCACAUGUAU------UUGUUUACUUGGCCG
....((((((((.((.((...))..)).)))))))).....((..(((((((((((((...))))------------...))))))))..------........)..)).. ( -28.00, z-score =   0.10, R)
>droVir3.scaffold_12875 19119555 77 + 20611582
CACACUGUAAGGACGCGUUCUGCUCUGACCUU--------------ACAUGUGCACGCCGUCC--------------CAUGCACAUGUAU------UUGUUUACUUGGCCG
..((..(((((((.((.....))))).....(--------------(((((((((.(......--------------).)))))))))).------....)))).)).... ( -17.40, z-score =  -0.10, R)
>droPer1.super_31 555606 110 - 935084
CUUAUUGUAAGGACACGCUCUGUUCUU-CUCUAUCCUUACGGUCGAACAUGUGCACGCUGCCACAUUAUAACAGCCGCGCGCACAUGUACGGGUAGUUGUUUACUCGGACG
.....((((((((..............-.....))))))))(((..((((((((.(((.((............)).))).)))))))).(((((((....)))))))))). ( -37.01, z-score =  -3.19, R)
>dp4.chr3 17412850 110 + 19779522
CUUAUUGUAAGGACACGCUCUGUUCUU-CUCUAUCCUUACGGUCGAACAUGUGCACGCUGCCACAUUAUAACAGCCGCGCGCACAUGUACGGGUAGUUGUUUACUCGGACG
.....((((((((..............-.....))))))))(((..((((((((.(((.((............)).))).)))))))).(((((((....)))))))))). ( -37.01, z-score =  -3.19, R)
>consensus
CUCACUGUAAGGACACGCUGUGCUCUGACCUUACAGCUG______AACAUGUGCGCGACGCCCUAUUAUCACAGCCGUGCGCACAUGUAU______UUGUUUACUUGGACG
......((((((.((.((...))..)).))))))............(((((((((((..((............))..)))))))))))....................... (-18.23 = -18.59 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,162,610 – 10,162,709
Length 99
Sequences 10
Columns 111
Reading direction reverse
Mean pairwise identity 77.05
Shannon entropy 0.46087
G+C content 0.50990
Mean single sequence MFE -36.33
Consensus MFE -15.53
Energy contribution -15.04
Covariance contribution -0.49
Combinations/Pair 1.41
Mean z-score -2.82
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979101
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10162610 99 - 21146708
CGUCCAAGUAAACAA------AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGCACAUGUU------CAGCUGUAAGGUCAGAGCACAGCGUGUCCUUACAGUGAG
...............------..(((((((((((((.((.........)).))).))))))))))(------((.((((((((.((..((...)).)).))))))))))). ( -38.60, z-score =  -3.33, R)
>droAna3.scaffold_13266 14512666 105 - 19884421
CGUCCAAGUAAACAA------AUACAUGUGCGCACGACUGUGAUAAUAGGACGUCGCGCACAUGUUCAUGUUCAGCUGUAAGGUCAGAGCUCAGCGUGUCCUUACAGUGAG
..........((((.------..(((((((((((((.((((....))))..))).))))))))))...))))..(((((((((.((..((...)).)).)))))))))... ( -41.50, z-score =  -4.27, R)
>droEre2.scaffold_4845 6909901 99 + 22589142
CGUCCAAGUAAACAA------AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGCACAUGUU------CAGCUGUAAGGUCAGAGCACAGCGUGUCCUUACAGUGAG
...............------..(((((((((((((.((.........)).))).))))))))))(------((.((((((((.((..((...)).)).))))))))))). ( -38.60, z-score =  -3.33, R)
>droYak2.chr2R 10099787 99 - 21139217
CGUCCAAGUAAACAA------AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGAACAUGUU------CAGCUGUAAGGUCAGAGUACAGCGUGUCCUUACAGUGAG
...............------..((((((.((((((.((.........)).))).))).))))))(------((.((((((((.((..(.....).)).))))))))))). ( -30.90, z-score =  -1.51, R)
>droSec1.super_1 7670266 99 - 14215200
CGUCCAAGUAAACAA------AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGCACAUGUU------CAGCUGUAAGGUCAGAGCACAGCGUGUCCUUACAGUGAG
...............------..(((((((((((((.((.........)).))).))))))))))(------((.((((((((.((..((...)).)).))))))))))). ( -38.60, z-score =  -3.33, R)
>droSim1.chr2R 8925506 99 - 19596830
CGUCCAAGUAAACAA------AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGCACAUGUU------AAGCUGUAAGGUCAGAGCACAGCGUGUCCUUACAGUGAG
...............------..(((((((((((((.((.........)).))).)))))))))).------..(((((((((.((..((...)).)).)))))))))... ( -38.20, z-score =  -3.37, R)
>droMoj3.scaffold_6496 12808570 93 - 26866924
CGGCCAAGUAAACAA------AUACAUGUGCAUA------------GCGCGCGGCGCGCACAUGUUCAGCUGUAGCUGUAAGGUCAGAGCAGAGCGCGUCCUUACAGUGCA
..((.......(((.------..((((((((...------------((((...)))))))))))).....))).(((((((((.....((.....))..))))))))))). ( -32.00, z-score =  -0.33, R)
>droVir3.scaffold_12875 19119555 77 - 20611582
CGGCCAAGUAAACAA------AUACAUGUGCAUG--------------GGACGGCGUGCACAUGU--------------AAGGUCAGAGCAGAACGCGUCCUUACAGUGUG
.((((..(....)..------.((((((((((((--------------......)))))))))))--------------).))))........((((.........)))). ( -25.20, z-score =  -1.76, R)
>droPer1.super_31 555606 110 + 935084
CGUCCGAGUAAACAACUACCCGUACAUGUGCGCGCGGCUGUUAUAAUGUGGCAGCGUGCACAUGUUCGACCGUAAGGAUAGAG-AAGAACAGAGCGUGUCCUUACAAUAAG
.(((((.(((......))).)).((((((((((((.((..(......)..)).))))))))))))..))).(((((((((...-............)))))))))...... ( -39.86, z-score =  -3.51, R)
>dp4.chr3 17412850 110 - 19779522
CGUCCGAGUAAACAACUACCCGUACAUGUGCGCGCGGCUGUUAUAAUGUGGCAGCGUGCACAUGUUCGACCGUAAGGAUAGAG-AAGAACAGAGCGUGUCCUUACAAUAAG
.(((((.(((......))).)).((((((((((((.((..(......)..)).))))))))))))..))).(((((((((...-............)))))))))...... ( -39.86, z-score =  -3.51, R)
>consensus
CGUCCAAGUAAACAA______AUACAUGUGCGCACGGCUGUGAUAAUAGGGCGUCGCGCACAUGUU______CAGCUGUAAGGUCAGAGCACAGCGUGUCCUUACAGUGAG
.......................((((((((((......................)))))))))).............(((((.....((.....))..)))))....... (-15.53 = -15.04 +  -0.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:22:11 2011