Locus 13156

Sequence ID dm3.chrX
Location 4,712,357 – 4,712,537
Length 180
Max. P 0.997439
window18080 window18081 window18082 window18083

overview

Window 0

Location 4,712,357 – 4,712,462
Length 105
Sequences 5
Columns 124
Reading direction forward
Mean pairwise identity 71.20
Shannon entropy 0.50202
G+C content 0.37566
Mean single sequence MFE -25.58
Consensus MFE -14.14
Energy contribution -14.22
Covariance contribution 0.08
Combinations/Pair 1.19
Mean z-score -1.58
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888711
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4712357 105 + 22422827
------------------CUCAU-UGAGGGAAAUGGGAAAAGCAUAUUAUAAUGUACUUUAGGACGCUUUACAAAGAAAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAA
------------------(((..-...((...((((((((((..........(((((((((.....(((....)))...((((......))))...)))))))))))))))))))))..))).. ( -22.50, z-score =  -1.81, R)
>droSim1.chrX 3635370 114 + 17042790
----------CCUCGAUUCUAAGUUCGCGUGAAUGGGAAAAGCUUUCUAUAAAGUACUUUAGGACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAAAA
----------.............(((.((.((.(((((((((.(((....)))((((((((....(((......))).(((((....).))))...)))))))).))))))))))))).))).. ( -25.90, z-score =  -0.99, R)
>droSec1.super_4 4156896 114 - 6179234
----------CCUCGAUUCUAAGUUCGCGUGAAUGGGAAAAGCUUUCUAUAAAGUACUUUAGGACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAA
----------.............(((.((.((.(((((((((.(((....)))((((((((....(((......))).(((((....).))))...)))))))).))))))))))))).))).. ( -25.60, z-score =  -0.53, R)
>droYak2.chrX 18043987 97 - 21770863
CAUGGGGGCACCUGGAUUCUAAGAUCGCUUGAAUGGGAAAAGCUUUU-----------------CGUUU----------AAAUAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCGGGGAGAA
...(((....))).((((....)))).(((((.(((((((((..(((-----------------..(((----------(((........))))))..)))....))))))))))))))..... ( -23.00, z-score =  -1.10, R)
>droEre2.scaffold_4690 2088918 110 + 18748788
-----------UCAAAUUCUAAGAUCGCAUGGCUGGGAAAAGCUUUUU-UAAUGUACUUUAGAACUCUUUACGUUGAA--AGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAGCUGGGAGAA
-----------.............((...(((((((((((((.(((((-(((((((....((....)).)))))))))--))).....(((((....)))))...)))))))))))))...)). ( -30.90, z-score =  -3.46, R)
>consensus
__________CCUCGAUUCUAAGAUCGCGUGAAUGGGAAAAGCUUUUUAUAAAGUACUUUAGGACGCUUCACGCAGAAAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAA
........................((.((...((((((((((.......................((........))...........(((((....)))))...)))))))))).)).))... (-14.14 = -14.22 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 4,712,357 – 4,712,462
Length 105
Sequences 5
Columns 124
Reading direction reverse
Mean pairwise identity 71.20
Shannon entropy 0.50202
G+C content 0.37566
Mean single sequence MFE -25.08
Consensus MFE -19.27
Energy contribution -18.84
Covariance contribution -0.43
Combinations/Pair 1.18
Mean z-score -2.28
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.10
SVM RNA-class probability 0.997439
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4712357 105 - 22422827
UUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUCCCUUUUUCUUUGUAAAGCGUCCUAAAGUACAUUAUAAUAUGCUUUUCCCAUUUCCCUCA-AUGAG------------------
.......((((((((((((((((((((((..((((.((.......)).)))))))))).((.(....).)).......))))))))))))))))......-.....------------------ ( -21.60, z-score =  -3.13, R)
>droSim1.chrX 3635370 114 - 17042790
UUUUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGGUUCCCUUUUGCUGCAUGAAGCGUCCUAAAGUACUUUAUAGAAAGCUUUUCCCAUUCACGCGAACUUAGAAUCGAGG----------
.....((.((((((((((((...((.....(((((((.((......((((......)))).....)).))))))).))...))))))))))))....(((........))).))---------- ( -27.70, z-score =  -1.59, R)
>droSec1.super_4 4156896 114 + 6179234
UUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGGUUCCCUUUUGCUGCAUGAAGCGUCCUAAAGUACUUUAUAGAAAGCUUUUCCCAUUCACGCGAACUUAGAAUCGAGG----------
.....((.((((((((((((...((.....(((((((.((......((((......)))).....)).))))))).))...))))))))))))....(((........))).))---------- ( -27.70, z-score =  -1.46, R)
>droYak2.chrX 18043987 97 + 21770863
UUCUCCCCGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUUAUUU----------AAACG-----------------AAAAGCUUUUCCCAUUCAAGCGAUCUUAGAAUCCAGGUGCCCCCAUG
........((((((((((((....((((..((((....))))..)----------)))..-----------------....))))))))))))...((.((((........))))))....... ( -21.70, z-score =  -2.32, R)
>droEre2.scaffold_4690 2088918 110 - 18748788
UUCUCCCAGCUGGGAAAAGUGUACUUUAUUUAAAGUGAUUUCCU--UUCAACGUAAAGAGUUCUAAAGUACAUUA-AAAAAGCUUUUCCCAGCCAUGCGAUCUUAGAAUUUGA-----------
........((((((((((((((((((((((((...(((......--.)))...))))......))))))))....-.....))))))))))))....................----------- ( -26.70, z-score =  -2.90, R)
>consensus
UUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUCCCUUUUGCUGCAUAAAGCGUCCUAAAGUACAUUAUAAAAAGCUUUUCCCAUUCACGCGAACUUAGAAUCGAGG__________
........((((((((((((.((((((....)))))).....((((........)))).......................))))))))))))............................... (-19.27 = -18.84 +  -0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,712,387 – 4,712,502
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 85.71
Shannon entropy 0.25163
G+C content 0.33674
Mean single sequence MFE -25.02
Consensus MFE -17.12
Energy contribution -17.96
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.19
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.815158
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4712387 115 + 22422827
UAAUGUACUUUAGGACGCUUUACAAAGAAAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCAAAUUUGCGUUAAAAUAAACAGCAAGAAA
...(((..((((.(((((...........(((((((...(((((....)))))....(((((((....))))))))))))))..........)))))....))))..)))..... ( -24.10, z-score =  -2.22, R)
>droSim1.chrX 3635409 115 + 17042790
UAAAGUACUUUAGGACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAAAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAA
..................(((.(((.((.(((((((...(((((....)))))....(((((((....))))))))))))))..)).......((((......))))))).))). ( -24.40, z-score =  -1.63, R)
>droSec1.super_4 4156935 115 - 6179234
UAAAGUACUUUAGGACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAA
..................(((.(((.((.(((((((...(((((....)))))....(((((((....))))))))))))))..)).......((((......))))))).))). ( -24.50, z-score =  -1.40, R)
>droYak2.chrX 18044018 106 - 21770863
------AAUGGGAAAAGCUUUUCGUUU---AAAUAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCGGGGAGAAUCCCUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAA
------.((((((((((..(((..(((---(((........))))))..)))....)))))))))).((((.....)))).........((((((((......))).)))))... ( -24.60, z-score =  -2.60, R)
>droEre2.scaffold_4690 2088955 113 + 18748788
UAAUGUACUUUAGAACUCUUUACGUUG--AAAGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAGCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAA
......................(((((--((((((....(((((....)))))....(((((((....)))))))))).))))))))..((((((((......))).)))))... ( -27.50, z-score =  -3.09, R)
>consensus
UAAAGUACUUUAGGACGCUUUACGCAG_AAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAA
......................(((...(((((((....(((((....)))))....(((((((....))))))))))))))..)))..((((((((......))).)))))... (-17.12 = -17.96 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,712,427 – 4,712,537
Length 110
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 90.59
Shannon entropy 0.16307
G+C content 0.33270
Mean single sequence MFE -21.05
Consensus MFE -17.04
Energy contribution -16.64
Covariance contribution -0.40
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533387
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4712427 110 + 22422827
CUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCAAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAA-----CAAAGAAUACC
...........((.((((((.(((..(((..((.....))..)))....((((((((......))).)))))...............))).)))))).)-----).......... ( -22.10, z-score =  -2.37, R)
>droSim1.chrX 3635449 110 + 17042790
CUUUAAAUAAAGUACACUUUUCCCAUCUGGGAAAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAA-----AAAAGAAUACC
..............((((((((((....))))).((((((((..((...(((((......)))))..))..((........)))))))))).)))))..-----........... ( -20.20, z-score =  -1.77, R)
>droSec1.super_4 4156975 110 - 6179234
CUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAA-----AAAAGAAUACC
..............((((((((((....))))))((((((((..((...(((((......)))))..))..((........))))))))))..))))..-----........... ( -20.30, z-score =  -1.55, R)
>droYak2.chrX 18044049 115 - 21770863
CUUUAAAUAAAGUACACUUUUCCCAUCGGGGAGAAUCCCUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAAAAAAAAUGGGGAAAAACACC
.................(((((((((..........((((((..((...((((((((......))).)))))....))......))))))..........)))))))))...... ( -20.35, z-score =  -0.87, R)
>droEre2.scaffold_4690 2088993 108 + 18748788
CUUUAAAUAAAGUACACUUUUCCCAGCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACGUCAAAAGGGUAAAA-------GGGAAAAAACACC
.................(((((((.((((..((.....))..))))...((((((((......))).))))).......................-------)))))))...... ( -22.30, z-score =  -1.58, R)
>consensus
CUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAA_____AAAAGAAUACC
...........((((..(((((((....)))))))..............((((((((......))).)))))....))))................................... (-17.04 = -16.64 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:15:41 2011