Locus 4257

Sequence ID dm3.chr2R
Location 11,725,802 – 11,725,928
Length 126
Max. P 0.965318
window5832 window5833 window5834 window5835

overview

Window 2

Location 11,725,802 – 11,725,897
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 84.26
Shannon entropy 0.29204
G+C content 0.45441
Mean single sequence MFE -22.57
Consensus MFE -16.14
Energy contribution -16.61
Covariance contribution 0.47
Combinations/Pair 1.16
Mean z-score -2.02
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886354
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725802 95 + 21146708
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAACAAAAAAAAAAAAGGAACAGAUAUU
(((...)))((((((((((.((....))))).......(((((.................)))))................)))))))....... ( -23.33, z-score =  -2.23, R)
>droSim1.chr2R 10465482 85 + 19596830
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAA----------AAAGGAACAGAUAUU
(((...)))((((((((((.((....))))).......(((((.................))))).....----------.)))))))....... ( -23.33, z-score =  -2.06, R)
>droSec1.super_1 9219952 85 + 14215200
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAA----------AAAGGAACAGAUAUU
(((...)))((((((((((.((....))))).......(((((.................))))).....----------.)))))))....... ( -23.33, z-score =  -2.06, R)
>droYak2.chr2R 3879806 91 - 21139217
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAAAAAAUG----AAAUAAGAAACAGAUAUU
(((((........((((((.((....))))))))....))))).....((((((.......))))))......----.................. ( -21.00, z-score =  -1.66, R)
>droEre2.scaffold_4845 8455330 88 - 22589142
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAAAAA-------AGAAAAAGAACAGAUAUU
(((...)))((((((((((.((....))))))))....(((((.................))))).....-------.......))))....... ( -21.63, z-score =  -2.09, R)
>droAna3.scaffold_13266 7414169 83 - 19884421
GCGGAGCCCCGUUCUUGCAAUCAGCAGAUGCAAGCCA-GCAUCGAAAAUUGUCCGAAAAAGGACAACAAA---------AAAUUGAGGAGAGG--
((((....))))((((.((((.....(((((......-))))).....((((((......))))))....---------..))))..))))..-- ( -22.80, z-score =  -2.03, R)
>consensus
GGGGCACCCGUUCCUUGCAAUCAGCAGAUGCAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAUAAA_________AAAAGGAACAGAUAUU
.((....))((((((((((.((....))))))))....(((((.................)))))...................))))....... (-16.14 = -16.61 +   0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,725,802 – 11,725,897
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 84.26
Shannon entropy 0.29204
G+C content 0.45441
Mean single sequence MFE -25.32
Consensus MFE -19.33
Energy contribution -19.80
Covariance contribution 0.47
Combinations/Pair 1.14
Mean z-score -2.28
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965318
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725802 95 - 21146708
AAUAUCUGUUCCUUUUUUUUUUUUGUUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..((((((((((............(((...(((((.((....))........)))))..)))(((((((....)).))))))))))))))).... ( -27.60, z-score =  -2.82, R)
>droSim1.chr2R 10465482 85 - 19596830
AAUAUCUGUUCCUUU----------UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..((((((((((((.----------.....(((((.((....))........)))))(..((........))..)....)))))))))))).... ( -26.20, z-score =  -2.50, R)
>droSec1.super_1 9219952 85 - 14215200
AAUAUCUGUUCCUUU----------UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..((((((((((((.----------.....(((((.((....))........)))))(..((........))..)....)))))))))))).... ( -26.20, z-score =  -2.50, R)
>droYak2.chr2R 3879806 91 + 21139217
AAUAUCUGUUUCUUAUUU----CAUUUUUUGUCCCUUUUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..................----......((((((.......)))))).....((((((((.((((((((....)).))))))...))))).))). ( -23.80, z-score =  -1.72, R)
>droEre2.scaffold_4845 8455330 88 + 22589142
AAUAUCUGUUCUUUUUCU-------UUUUUGUCCCUUUUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..(((((((((...((((-------...((((((.......)))))).....)))).....((((((((....)).))))))))))))))).... ( -25.00, z-score =  -2.31, R)
>droAna3.scaffold_13266 7414169 83 + 19884421
--CCUCUCCUCAAUUU---------UUUGUUGUCCUUUUUCGGACAAUUUUCGAUGC-UGGCUUGCAUCUGCUGAUUGCAAGAACGGGGCUCCGC
--.....((((.....---------...(((((((......))))))).((((((((-......)))))(((.....))).))).))))...... ( -23.10, z-score =  -1.86, R)
>consensus
AAUAUCUGUUCCUUUU_________UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUGCAUCUGCUGAUUGCAAGGAACGGGUGCCCC
..(((((((((..................(((((.......)))))...............((((((((....)).))))))))))))))).... (-19.33 = -19.80 +   0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,725,832 – 11,725,928
Length 96
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.63
Shannon entropy 0.39810
G+C content 0.37032
Mean single sequence MFE -15.08
Consensus MFE -7.60
Energy contribution -8.96
Covariance contribution 1.36
Combinations/Pair 1.08
Mean z-score -2.01
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711145
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725832 96 + 21146708
CAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAACAAAAAAAAAAAAGGAACAGAUAUUUAUAUAUAUAAAGACAAAGGCGAUUUCAGUG---
...(((..(((((.................)))))............................(((((....)))))......)))..........--- ( -13.83, z-score =  -1.84, R)
>droSim1.chr2R 10465512 84 + 19596830
CAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAA----------AAAGGAACAGAUAUUUAUAUAUA--AAGACAAAGGCGAUUUCAGUG---
...(((..((.((......(((((.......)))))....----------...)).))..((((....)))).--........)))..........--- ( -15.02, z-score =  -2.20, R)
>droSec1.super_1 9219982 84 + 14215200
CAAGCCAAGUCCCGAAAAUUGUCCGAAGAAGGGACAUAAA----------AAAGGAACAGAUAUUUAUAUAUA--AAGACAAAGGCGAUUUCAGUG---
...(((..((.((......(((((.......)))))....----------...)).))..((((....)))).--........)))..........--- ( -15.02, z-score =  -2.20, R)
>droYak2.chr2R 3879836 90 - 21139217
CAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAAAAA----AUGAAAUAAGAAACAGAUAUUUAUAUAUA--GAGGCAGAGGCGAUUUCAGUG---
...(((..(((.(.....((((((.......))))))...----................((((....)))).--).)))...)))..........--- ( -13.80, z-score =  -1.15, R)
>droEre2.scaffold_4845 8455360 87 - 22589142
CAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAAAAA-------AGAAAAAGAACAGAUAUUUAUAUAUA--AAGACAAAGGCGAUUUCAGUG---
...(((..(((.......((((((.......))))))...-------.............((((....)))).--..)))...)))..........--- ( -13.80, z-score =  -2.31, R)
>droAna3.scaffold_13266 7414199 82 - 19884421
CAAGCCA-GCAUCGAAAAUUGUCCGAAAAAGGACAACAAA--------------AAAUUGAGGAGAGGAGACA--AGGACCAGGAGGACUUUGUUGAUG
.......-.((((.....((((((......))))))....--------------...............((((--(((.((....)).))))))))))) ( -19.00, z-score =  -2.37, R)
>consensus
CAAGCCAAGUCCCGAAAAUUGUCCGAAAAAGGGACAUAAA__________AAAGGAACAGAUAUUUAUAUAUA__AAGACAAAGGCGAUUUCAGUG___
...(((..(((((.................))))).........................((((....))))...........)))............. ( -7.60 =  -8.96 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,725,832 – 11,725,928
Length 96
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 77.63
Shannon entropy 0.39810
G+C content 0.37032
Mean single sequence MFE -14.49
Consensus MFE -7.81
Energy contribution -8.65
Covariance contribution 0.84
Combinations/Pair 1.29
Mean z-score -1.87
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.729958
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11725832 96 - 21146708
---CACUGAAAUCGCCUUUGUCUUUAUAUAUAUAAAUAUCUGUUCCUUUUUUUUUUUUGUUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUG
---..........(((...(((((.......(((((((...................)))))))((((.......)))).......)))))..)))... ( -15.31, z-score =  -2.02, R)
>droSim1.chr2R 10465512 84 - 19596830
---CACUGAAAUCGCCUUUGUCUU--UAUAUAUAAAUAUCUGUUCCUUU----------UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUG
---..........((((((((...--.....))))).....(((((...----------....(((((.......)))))......)))))..)))... ( -14.12, z-score =  -1.74, R)
>droSec1.super_1 9219982 84 - 14215200
---CACUGAAAUCGCCUUUGUCUU--UAUAUAUAAAUAUCUGUUCCUUU----------UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUG
---..........((((((((...--.....))))).....(((((...----------....(((((.......)))))......)))))..)))... ( -14.12, z-score =  -1.74, R)
>droYak2.chr2R 3879836 90 + 21139217
---CACUGAAAUCGCCUCUGCCUC--UAUAUAUAAAUAUCUGUUUCUUAUUUCAU----UUUUUGUCCCUUUUUCGGACAAUUUUCGGGACUUGGCUUG
---..........(((....(((.--.......(((((.........)))))...----...((((((.......)))))).....)))....)))... ( -13.30, z-score =  -1.21, R)
>droEre2.scaffold_4845 8455360 87 + 22589142
---CACUGAAAUCGCCUUUGUCUU--UAUAUAUAAAUAUCUGUUCUUUUUCU-------UUUUUGUCCCUUUUUCGGACAAUUUUCGGGACUUGGCUUG
---..........(((...(((((--.((((....)))).............-------...((((((.......)))))).....)))))..)))... ( -14.20, z-score =  -2.05, R)
>droAna3.scaffold_13266 7414199 82 + 19884421
CAUCAACAAAGUCCUCCUGGUCCU--UGUCUCCUCUCCUCAAUUU--------------UUUGUUGUCCUUUUUCGGACAAUUUUCGAUGC-UGGCUUG
((((.((((.(.((....)).).)--)))................--------------...(((((((......)))))))....)))).-....... ( -15.90, z-score =  -2.44, R)
>consensus
___CACUGAAAUCGCCUUUGUCUU__UAUAUAUAAAUAUCUGUUCCUUU__________UUUAUGUCCCUUCUUCGGACAAUUUUCGGGACUUGGCUUG
.............(((...(((((...((((....))))........................(((((.......)))))......)))))..)))... ( -7.81 =  -8.65 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:42 2011