Locus 2700

Sequence ID dm3.chr2L
Location 21,232,542 – 21,232,608
Length 66
Max. P 0.773842
window3699 window3700

overview

Window 9

Location 21,232,542 – 21,232,608
Length 66
Sequences 10
Columns 86
Reading direction forward
Mean pairwise identity 69.70
Shannon entropy 0.57293
G+C content 0.39678
Mean single sequence MFE -15.70
Consensus MFE -3.71
Energy contribution -3.81
Covariance contribution 0.10
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.24
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.773842
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21232542 66 + 23011544
ACAACAAAUAUUCAACAACAAUGG---------GCGACGG-CACUUGUUAAUUUAACAAGCUGUCACCACUCAAAU----------
.......................(---------(.(((((-(..((((((...)))))))))))).))........---------- ( -14.80, z-score =  -3.86, R)
>droSim1.chr2L 20817135 66 + 22036055
ACAACAAAUAUUCAACAACAAUGG---------GUGACGG-UACUUGUUAAUUUAACAAGCUGUCACCACUCAAAG----------
.......................(---------(((((((-..(((((((...)))))))))))))))........---------- ( -17.90, z-score =  -4.24, R)
>droSec1.super_18 1157347 66 + 1342155
ACAACAAAUAUUCAACAACAAUGG---------GCGACGG-UACUUGUUAAUUUAACAAGCUGUCACCACUCCAAU----------
.......................(---------(.(((((-..(((((((...)))))))))))).))........---------- ( -14.00, z-score =  -2.93, R)
>droYak2.chr2R 19596855 65 - 21139217
ACAACAAAUUUUCAACAACAAUGG---------GCGGCG--CACUUGUUAAUUUAACAAGCUGUCACCACGCAAGU----------
.......................(---------(.((((--..(((((((...))))))).)))).))((....))---------- ( -12.70, z-score =  -1.16, R)
>droEre2.scaffold_4845 19323386 66 - 22589142
ACAACAAAUAUUCAACAACAAUGG---------GCGACGG-CACUUGUUAAUUUAACAAGCUGUCACCACGCAAAU----------
.......................(---------(.(((((-(..((((((...)))))))))))).))........---------- ( -14.80, z-score =  -3.20, R)
>droAna3.scaffold_12916 10971511 56 + 16180835
ACAACAA-CAUUCAACAAUAAUGA---------GUGGCAGUCACUUGUUAAUUUAACAAGCUGCCG--------------------
.......-.(((((.......)))---------))(((((...(((((((...)))))))))))).-------------------- ( -14.10, z-score =  -3.12, R)
>dp4.chr4_group4 3319624 84 + 6586962
ACAACAAAUAAUCAACAACAAUGAAGA--GGGAGAGAAGGCCGCUUGUUAAUUUAACAAGCGGGCGAGUCGAUCCUCCCCUCCCGU
.........................((--(((.(((..(.((((((((((...)))))))))).)((.....)))))))))).... ( -28.30, z-score =  -3.94, R)
>droWil1.scaffold_180772 7226497 73 + 8906247
ACAACAAAAUAUCAACAACAAAGAUGAAGGGGGGAAAUGAUCGCUUGUUAAUUUAACAAGUCGCAUAUCCUGU-------------
.........((((.........)))).....((((.(((...((((((((...))))))))..))).))))..------------- ( -14.00, z-score =  -1.76, R)
>droMoj3.scaffold_6500 18521002 67 - 32352404
ACAACAGAUGAUCAACAACAAGGU--------GCCGGAGGUCACUUGUUAAUUUAACAAGC-GGUGCUCCAAAGAU----------
.....................((.--------.((((....).(((((((...))))))))-))..))........---------- ( -11.90, z-score =   0.04, R)
>droGri2.scaffold_15252 14176818 68 - 17193109
ACAACAAAUGAUCAACAACAAAAUA-------GGCGGAGGCCACUUGUUAAUUUAACAAAC-GGCUCUCCUGAGAU----------
.........................-------...(((((((..((((((...))))))..-))).))))......---------- ( -14.50, z-score =  -2.48, R)
>consensus
ACAACAAAUAUUCAACAACAAUGG_________GCGACGG_CACUUGUUAAUUUAACAAGCUGUCACCACUCAAAU__________
...........................................(((((((...))))))).......................... ( -3.71 =  -3.81 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 21,232,542 – 21,232,608
Length 66
Sequences 10
Columns 86
Reading direction reverse
Mean pairwise identity 69.70
Shannon entropy 0.57293
G+C content 0.39678
Mean single sequence MFE -17.20
Consensus MFE -5.67
Energy contribution -5.60
Covariance contribution -0.07
Combinations/Pair 1.25
Mean z-score -1.96
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.656440
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21232542 66 - 23011544
----------AUUUGAGUGGUGACAGCUUGUUAAAUUAACAAGUG-CCGUCGC---------CCAUUGUUGUUGAAUAUUUGUUGU
----------......(.((((((.((((((((...)))))))).-..)))))---------))...................... ( -16.70, z-score =  -2.42, R)
>droSim1.chr2L 20817135 66 - 22036055
----------CUUUGAGUGGUGACAGCUUGUUAAAUUAACAAGUA-CCGUCAC---------CCAUUGUUGUUGAAUAUUUGUUGU
----------......(.((((((.((((((((...)))))))).-..)))))---------))...................... ( -16.00, z-score =  -2.15, R)
>droSec1.super_18 1157347 66 - 1342155
----------AUUGGAGUGGUGACAGCUUGUUAAAUUAACAAGUA-CCGUCGC---------CCAUUGUUGUUGAAUAUUUGUUGU
----------......(.((((((.((((((((...)))))))).-..)))))---------))...................... ( -15.60, z-score =  -1.61, R)
>droYak2.chr2R 19596855 65 + 21139217
----------ACUUGCGUGGUGACAGCUUGUUAAAUUAACAAGUG--CGCCGC---------CCAUUGUUGUUGAAAAUUUGUUGU
----------...((.((((((...((((((((...)))))))).--))))))---------.))..................... ( -17.60, z-score =  -1.65, R)
>droEre2.scaffold_4845 19323386 66 + 22589142
----------AUUUGCGUGGUGACAGCUUGUUAAAUUAACAAGUG-CCGUCGC---------CCAUUGUUGUUGAAUAUUUGUUGU
----------......(.((((((.((((((((...)))))))).-..)))))---------))...................... ( -16.80, z-score =  -1.91, R)
>droAna3.scaffold_12916 10971511 56 - 16180835
--------------------CGGCAGCUUGUUAAAUUAACAAGUGACUGCCAC---------UCAUUAUUGUUGAAUG-UUGUUGU
--------------------.((((((((((((...)))))))...)))))..---------(((.......)))...-....... ( -13.10, z-score =  -1.31, R)
>dp4.chr4_group4 3319624 84 - 6586962
ACGGGAGGGGAGGAUCGACUCGCCCGCUUGUUAAAUUAACAAGCGGCCUUCUCUCCC--UCUUCAUUGUUGUUGAUUAUUUGUUGU
..(((((((((((..........((((((((((...)))))))))))))))))))))--........................... ( -31.90, z-score =  -3.72, R)
>droWil1.scaffold_180772 7226497 73 - 8906247
-------------ACAGGAUAUGCGACUUGUUAAAUUAACAAGCGAUCAUUUCCCCCCUUCAUCUUUGUUGUUGAUAUUUUGUUGU
-------------((((((((..((.(((((((...)))))))))..............(((.(......).)))))))))))... ( -11.50, z-score =  -0.94, R)
>droMoj3.scaffold_6500 18521002 67 + 32352404
----------AUCUUUGGAGCACC-GCUUGUUAAAUUAACAAGUGACCUCCGGC--------ACCUUGUUGUUGAUCAUCUGUUGU
----------......((((...(-((((((((...)))))))))..))))(((--------(...((........))..)))).. ( -15.00, z-score =  -1.16, R)
>droGri2.scaffold_15252 14176818 68 + 17193109
----------AUCUCAGGAGAGCC-GUUUGUUAAAUUAACAAGUGGCCUCCGCC-------UAUUUUGUUGUUGAUCAUUUGUUGU
----------......((((.(((-((((((((...)))))))))))))))...-------......................... ( -17.80, z-score =  -2.74, R)
>consensus
__________AUUUGAGUGGUGACAGCUUGUUAAAUUAACAAGUG_CCGUCGC_________CCAUUGUUGUUGAAUAUUUGUUGU
.........................((((((((...)))))))).......................................... ( -5.67 =  -5.60 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:06 2011