Locus 10334

Sequence ID dm3.chr3R
Location 13,118,204 – 13,118,313
Length 109
Max. P 0.893338
window14208 window14209

overview

Window 8

Location 13,118,204 – 13,118,313
Length 109
Sequences 12
Columns 116
Reading direction forward
Mean pairwise identity 67.40
Shannon entropy 0.68611
G+C content 0.53588
Mean single sequence MFE -34.43
Consensus MFE -6.69
Energy contribution -6.70
Covariance contribution 0.01
Combinations/Pair 1.17
Mean z-score -2.57
Structure conservation index 0.19
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.780820
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13118204 109 + 27905053
---GCUUCUGA---CUCCCUGGAUACUUUCCACGGAGUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCCCC-ACCAUCUGACAUAUUUGACUUCGCGUGCUCUUU
---(((..(((---((((.((((.....)))).)))))))..))).......((((((.....(((.((..((.((((....-.)))).))...)).))).....))))))..... ( -39.70, z-score =  -4.71, R)
>dp4.chr2 21484211 106 - 30794189
---GCCACUG------CCGCGGAUACCUCAAGCGGAUUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCACC-ACCAUCUGACUUAUUGCCCUUCGUGUGCUCUUU
---(((..((------((..((((.((......))))))..).)))..)))((((((...(.(((((.((.((.((((....-.)))).)).)).))))))...))))))...... ( -30.80, z-score =  -1.00, R)
>droPer1.super_0 8705454 106 - 11822988
---GCCACUG------CCGCGGAUACCUCAAGCGGAUUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCACC-ACCAUCUGACUUAUUGCCCUUCGUGUGCUCUUU
---(((..((------((..((((.((......))))))..).)))..)))((((((...(.(((((.((.((.((((....-.)))).)).)).))))))...))))))...... ( -30.80, z-score =  -1.00, R)
>droEre2.scaffold_4770 9237096 108 - 17746568
---GCCGCUGA---CUCCCUGGUUGC-UUCCACGGACUCAAGAGCAACGGCCGCACGUCCGUGCAAUUAGCCAAAUGGCCCC-ACCAUCUGAGUUAUUUGACUUCGCGUGCUCGUG
---(((..(((---.(((.(((....-..))).))).))).).)).((((..((((((.....(((.((((((.((((....-.)))).)).)))).))).....)))))))))). ( -34.00, z-score =  -1.37, R)
>droYak2.chr3R 17208667 109 + 28832112
---GCUCCUGA---CUCCCUGGACGCCUUCCACGGAGUCAAGAACAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCCCC-ACCAUCUGAGUUAUUUGACUUCGCAUGCUCUUU
---((((.(((---((((.((((.....)))).))))))).))......((.((((....))))...((((((.((((....-.)))).)).)))).........))..))..... ( -33.00, z-score =  -2.52, R)
>droSec1.super_12 1095471 109 - 2123299
---GCUCCUGA---CUCCCUGGAUACUUUCCACGGAGUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCCCC-ACCAUCUGACAUAUUUGACUUCGGCUGCUCUUU
---((((.(((---((((.((((.....)))).))))))).))))..(((((((((....)))).....(((....)))...-......................)))))...... ( -43.70, z-score =  -5.87, R)
>droSim1.chr3R 19163904 109 - 27517382
---GCUCUUGA---CUCCCUGGAUACUUUCCACGGAGUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCCCC-ACCAUCUGACAUAUUUGACUUUGGGUGCUCUUU
---((((((((---((((.((((.....)))).))))))))))))...(((.((((....)))).....)))(((.((((((-(...((..........))...)))).))).))) ( -46.20, z-score =  -6.09, R)
>droMoj3.scaffold_6540 17638564 99 + 34148556
CUAGGCGCUGGGUCAUGCCCCAACAUCGUCGGCGUGCC----GUCGAUGUCAACACGUUCGUGCAAUUAGCCAAAUGGCUCC-ACGGUCUGACUUGUGCCCUUU------------
...(((((.((((((.(((...((((((.(((....))----).))))))..........(((.....((((....)))).)-))))).)))))))))))....------------ ( -39.00, z-score =  -2.82, R)
>droVir3.scaffold_13047 14214183 93 + 19223366
---GCCGCAGGGUCAUGUCCUGGCAAC---GGCGUGCC----GUCGAUGCCUGCACGUACUUGCAAUUAGCCAAAUGGCUCC-ACGGGCUGACUUGUAUCCUUU------------
---...(((((.(((.((((.((((.(---((((...)----)))).))))((((......))))...((((....))))..-..)))))))))))).......------------ ( -32.40, z-score =  -0.52, R)
>droGri2.scaffold_14830 530967 93 - 6267026
---GCUGUUGGGUCAUGUCCUGACAUC---GGCGUGUC----GUCGAUGUCUGCACGUUCUUGUAAUUAGCCAAAUGGCUCC-ACGAUCUGACUUGUGUCUCUU------------
---((.((..((((((((.(.((((((---((((...)----))))))))).).))))..........((((....))))..-..))))..))..)).......------------ ( -31.40, z-score =  -2.97, R)
>droWil1.scaffold_181089 1718051 103 + 12369635
---GCAGCAGAA---UGCUUGUAUUCACCCUGUAGAUUCAAGAGCAAUGCCCGCACGUUCGUGCAAUUAGCCAAAUGGCCUCAACAGUCUGACUUUUUGCCUGCCCUUU-------
---(((((((((---((....)))))......((((((...(((........((((....)))).....(((....))))))...))))))......)).)))).....------- ( -25.10, z-score =  -0.82, R)
>droAna3.scaffold_13340 10334703 113 + 23697760
---GCUCCCGGUUUCUCCCUGGAUAUUUUCGACGAAGUCAAGAGCAAUGGCCGCACGUUCUUGCAAUUAGCCAAAUGGCCCCCAACAUCUGACUUAUUGUUUUCCGUGUGUUUCCG
---((((((((.......))))........(((...)))..))))...((.((((((.....(((((.((.((.(((........))).)).)).)))))....))))))...)). ( -27.10, z-score =  -1.10, R)
>consensus
___GCUGCUGA___CUCCCUGGAUACCUUCCACGGAGUCAAGAGCAACGGCCGCACGUUCGUGCAAUUAGCCAAAUGGCCCC_ACCAUCUGACUUAUUUCACUUCGUGUGCUCUUU
....................................................(((......))).....(((....)))..................................... ( -6.69 =  -6.70 +   0.01)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 9

Location 13,118,204 – 13,118,313
Length 109
Sequences 12
Columns 116
Reading direction reverse
Mean pairwise identity 67.40
Shannon entropy 0.68611
G+C content 0.53588
Mean single sequence MFE -39.59
Consensus MFE -8.37
Energy contribution -8.37
Covariance contribution -0.01
Combinations/Pair 1.62
Mean z-score -2.66
Structure conservation index 0.21
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.893338
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13118204 109 - 27905053
AAAGAGCACGCGAAGUCAAAUAUGUCAGAUGGU-GGGGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGACUCCGUGGAAAGUAUCCAGGGAG---UCAGAAGC---
.(((((((.(((..(((......(((((((((.-....))))))))).....((((....)))))))))))))))))((((((.((((.....)))).))))---))......--- ( -49.50, z-score =  -5.34, R)
>dp4.chr2 21484211 106 + 30794189
AAAGAGCACACGAAGGGCAAUAAGUCAGAUGGU-GGUGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGAAUCCGCUUGAGGUAUCCGCGG------CAGUGGC---
.....((.(((.(((((((((.((((((((((.-....))))))))))..((((((....))))))..)))))))))....((((..((....)).))))------..)))))--- ( -40.90, z-score =  -1.90, R)
>droPer1.super_0 8705454 106 + 11822988
AAAGAGCACACGAAGGGCAAUAAGUCAGAUGGU-GGUGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGAAUCCGCUUGAGGUAUCCGCGG------CAGUGGC---
.....((.(((.(((((((((.((((((((((.-....))))))))))..((((((....))))))..)))))))))....((((..((....)).))))------..)))))--- ( -40.90, z-score =  -1.90, R)
>droEre2.scaffold_4770 9237096 108 + 17746568
CACGAGCACGCGAAGUCAAAUAACUCAGAUGGU-GGGGCCAUUUGGCUAAUUGCACGGACGUGCGGCCGUUGCUCUUGAGUCCGUGGAA-GCAACCAGGGAG---UCAGCGGC---
.(((.((.((((..(((........(((((((.-....)))))))((.....))...))).))))))))).(((.((((.(((.(((..-....))).))).---)))).)))--- ( -40.40, z-score =  -1.36, R)
>droYak2.chr3R 17208667 109 - 28832112
AAAGAGCAUGCGAAGUCAAAUAACUCAGAUGGU-GGGGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGUUCUUGACUCCGUGGAAGGCGUCCAGGGAG---UCAGGAGC---
...(((.................))).((((((-..((((....))))...(((((....)))))))))))((((((((((((.((((.....)))).))))---))))))))--- ( -44.63, z-score =  -3.32, R)
>droSec1.super_12 1095471 109 + 2123299
AAAGAGCAGCCGAAGUCAAAUAUGUCAGAUGGU-GGGGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGACUCCGUGGAAAGUAUCCAGGGAG---UCAGGAGC---
....(((.(((............(((((((((.-....))))))))).....((((....))))))).)))((((((((((((.((((.....)))).))))---))))))))--- ( -54.10, z-score =  -6.42, R)
>droSim1.chr3R 19163904 109 + 27517382
AAAGAGCACCCAAAGUCAAAUAUGUCAGAUGGU-GGGGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGACUCCGUGGAAAGUAUCCAGGGAG---UCAAGAGC---
...(.((.((((..(((..........)))..)-))))))....((((....((((....))))))))...((((((((((((.((((.....)))).))))---))))))))--- ( -50.70, z-score =  -5.84, R)
>droMoj3.scaffold_6540 17638564 99 - 34148556
------------AAAGGGCACAAGUCAGACCGU-GGAGCCAUUUGGCUAAUUGCACGAACGUGUUGACAUCGAC----GGCACGCCGACGAUGUUGGGGCAUGACCCAGCGCCUAG
------------...((((.(..((((...(((-(.((((....)))).....))))...((.(..((((((.(----((....))).))))))..).)).))))...).)))).. ( -39.30, z-score =  -2.71, R)
>droVir3.scaffold_13047 14214183 93 - 19223366
------------AAAGGAUACAAGUCAGCCCGU-GGAGCCAUUUGGCUAAUUGCAAGUACGUGCAGGCAUCGAC----GGCACGCC---GUUGCCAGGACAUGACCCUGCGGC---
------------..(((...((.(((.(((...-..((((....))))...((((......)))))))..((((----((....))---))))....))).))..))).....--- ( -27.80, z-score =   0.66, R)
>droGri2.scaffold_14830 530967 93 + 6267026
------------AAGAGACACAAGUCAGAUCGU-GGAGCCAUUUGGCUAAUUACAAGAACGUGCAGACAUCGAC----GACACGCC---GAUGUCAGGACAUGACCCAACAGC---
------------....(((....)))......(-((((((....))))...........(((((.(((((((.(----(...)).)---))))))..).))))..))).....--- ( -24.10, z-score =  -1.94, R)
>droWil1.scaffold_181089 1718051 103 - 12369635
-------AAAGGGCAGGCAAAAAGUCAGACUGUUGAGGCCAUUUGGCUAAUUGCACGAACGUGCGGGCAUUGCUCUUGAAUCUACAGGGUGAAUACAAGCA---UUCUGCUGC---
-------.((((((((((....(((((((..((....))..)))))))..((((((....)))))))).)))))))).......(((((((........))---)))))....--- ( -31.20, z-score =  -0.89, R)
>droAna3.scaffold_13340 10334703 113 - 23697760
CGGAAACACACGGAAAACAAUAAGUCAGAUGUUGGGGGCCAUUUGGCUAAUUGCAAGAACGUGCGGCCAUUGCUCUUGACUUCGUCGAAAAUAUCCAGGGAGAAACCGGGAGC---
.((...(.((((.....((((.(((((((((........))))))))).))))......)))).).))...(((((((.((((.(.((.....)).).))))....)))))))--- ( -31.50, z-score =  -0.96, R)
>consensus
AAAGAGCACACGAAGGGAAAUAAGUCAGAUGGU_GGGGCCAUUUGGCUAAUUGCACGAACGUGCGGCCGUUGCUCUUGACUCCGCGGAAGGUAUCCAGGGAG___UCAGCAGC___
...........................((((.....((((....))))..(((((......))))).........................))))..................... ( -8.37 =  -8.37 +  -0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:57 2011