Locus 14180

Sequence ID dm3.chrX
Location 11,659,906 – 11,660,035
Length 129
Max. P 0.979064
window19524 window19525 window19526

overview

Window 4

Location 11,659,906 – 11,660,003
Length 97
Sequences 8
Columns 103
Reading direction forward
Mean pairwise identity 63.80
Shannon entropy 0.72506
G+C content 0.52125
Mean single sequence MFE -24.78
Consensus MFE -10.44
Energy contribution -10.68
Covariance contribution 0.24
Combinations/Pair 1.44
Mean z-score -0.92
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.732628
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 11659906 97 + 22422827
-----AGGUUCCAGUUAGAUCCCCCUCAAAAAGCCAAACGGAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCAUCCAAAAGG
-----.((.((......)).)).(((......((((.....(((.(((((((.((((((..........)))))).)))))))-.)))))))........))) ( -21.54, z-score =   0.64, R)
>droPer1.super_28 412208 93 - 1111753
GAGAUCGGGACAGACCAGUUUCUAAAGCG-CGGCCAAACGGAUGCGGACCAGGUGGAAUUCGCUUUCUCAUUUCGAUUGGCCU-UUAUUGGCCAU--------
(((((.((((.((.(.((((((.....((-((.((....)).))))........)))))).))).)))))))))...(((((.-.....))))).-------- ( -26.72, z-score =  -0.23, R)
>dp4.chrXL_group1a 6887832 93 - 9151740
GAGAUCGGGACAGACCAGUUUCUAAAGCG-CGGCCAAACGGAUGCGGACCAGGUGGAAUUCGCUUUCUCAUUUCGAUUGGCCU-UUAUUGGCCAU--------
(((((.((((.((.(.((((((.....((-((.((....)).))))........)))))).))).)))))))))...(((((.-.....))))).-------- ( -26.72, z-score =  -0.23, R)
>droAna3.scaffold_13417 1407997 73 + 6960332
------------------UGCACACAGCGACUGCCAAACGGAUGCAGGCCAA---GAAUUCGCUUUCCCAUUUCGAUUGGCCGAUUGGAGGCUG---------
------------------.((...(((((.(((.....))).))).(((((.---(((.............)))...)))))...))...))..--------- ( -16.72, z-score =   0.79, R)
>droEre2.scaffold_4690 15208781 95 - 18748788
-----AGGUUCCAGCCAGAUCCCC-UCAAAAACCAAAACGGAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCACCGAAAUG-
-----.((((((((((.(((((..-..............)))).).)))....)))))))........(((((((..(((((.-.....))))).)))))))- ( -27.09, z-score =  -1.53, R)
>droSec1.super_36 335510 96 + 449511
-----UGGUUCCAGUUAGAUCCCCCUCAAAAAGCCAAACGGAUGCUGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCAUCGAAAUG-
-----(((..(((((...((((.................))))))))))))...((((......))))(((((((((.((((.-.....)))))))))))))- ( -30.93, z-score =  -2.51, R)
>droSim1.chrX 8976534 96 + 17042790
-----UGGUUCCAGUUAGAUCCCCCUCAAAAAGCCAAACGGAUGCUGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCAUCGAAAUG-
-----(((..(((((...((((.................))))))))))))...((((......))))(((((((((.((((.-.....)))))))))))))- ( -30.93, z-score =  -2.51, R)
>droGri2.scaffold_14853 8345402 95 - 10151454
--GCCCCUGCCCCCCCCCCCCCCGCCCUUUCCCCCGCACGUG-ACUGGACUGCUGGAAUUUGCUUUCUCGUUUGUGCUG-CCAAAUGUUGAAAGCUUUG----
--..............................((.(((.((.-.....))))).)).....((((((.((((((.....-.))))))..))))))....---- ( -17.60, z-score =  -1.83, R)
>consensus
_____CGGUUCCAGCCAGAUCCCCCUCAAAAAGCCAAACGGAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU_UCAUUGGCCAUC_AA____
......................................((((....((..(((((.....)))))..))..))))..(((((.......)))))......... (-10.44 = -10.68 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,659,941 – 11,660,035
Length 94
Sequences 7
Columns 98
Reading direction forward
Mean pairwise identity 70.77
Shannon entropy 0.54608
G+C content 0.55508
Mean single sequence MFE -31.90
Consensus MFE -20.66
Energy contribution -20.26
Covariance contribution -0.40
Combinations/Pair 1.43
Mean z-score -1.53
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979064
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11659941 94 + 22422827
GAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCAU-CCAAAAGGGGGGGAACUGAGGACUGCAGACCGAAGACCAG--
..(((((.((.(((........((..(((.(((.(((.((((.-.....))))))-).))).)))..)).)))..)).))))).............-- ( -32.00, z-score =  -0.94, R)
>droPer1.super_28 412247 76 - 1111753
GAUGCGGACCAGGUGGAAUUCGCUUUCUCAUUUCGAUUGGCCU-UUAUUGGCCA---UGGCCGAGGGGCUGCUG----CUGCGG--------------
....(((.((((((((((......))).)))).....(((((.-.....)))))---)))))).(.(((....)----)).)..-------------- ( -24.20, z-score =   0.24, R)
>dp4.chrXL_group1a 6887871 76 - 9151740
GAUGCGGACCAGGUGGAAUUCGCUUUCUCAUUUCGAUUGGCCU-UUAUUGGCCA---UGGCCGAGGGGCUGCUG----CUGCGG--------------
....(((.((((((((((......))).)))).....(((((.-.....)))))---)))))).(.(((....)----)).)..-------------- ( -24.20, z-score =   0.24, R)
>droAna3.scaffold_13417 1408019 85 + 6960332
GAUGCAGGCCAA---GAAUUCGCUUUCCCAUUUCGAUUGGCCGAUUGGAGGCUGGAGAGGAUCGGGGGCGAGCGAGAUUCGGGGGAAU----------
........((..---((((((((((((((..(((..(..(((.......)))..)...)))...)))).)))))).))))..))....---------- ( -29.60, z-score =  -0.69, R)
>droEre2.scaffold_4690 15208815 88 - 18748788
GAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCA--CCGAAAUGGGGGGAUUCGAAGACUGCAGACCGAGG-------
..(((((.((....))..((((.(..(((((((((..(((((.-.....)))))--.)))))))))..)...))))..)))))........------- ( -36.80, z-score =  -3.02, R)
>droSec1.super_36 335545 95 + 449511
GAUGCUGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCA--UCGAAAUGGGGGGAACUGAGGACAGCAGACCGAAGACCGAAG
..(((((.((..(((.....)))(..(((((((((((.((((.-.....)))))--))))))))))..)......)).)))))............... ( -40.10, z-score =  -3.64, R)
>droSim1.chrX 8976569 95 + 17042790
GAUGCUGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU-UCAUUGGCCA--UCGAAAUGGGGGGAACUGAGGACAACAGACCGAAGACCGAAG
...(((.....)))((..((((.(..(((((((((((.((((.-.....)))))--))))))))))..)..(((.......)))..))))..)).... ( -36.40, z-score =  -2.92, R)
>consensus
GAUGCAGGCCAAGUGGAAUUCGCUUUCCCAUUUCGAUUGGCCU_UCAUUGGCCA___CGAAAGGGGGGGAACUGAGGACUGCAGACCGA_G_______
..(((((...(((((.....)))))((((..((((..(((((.......)))))...))))...))))..........)))))............... (-20.66 = -20.26 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 11,659,941 – 11,660,035
Length 94
Sequences 7
Columns 98
Reading direction reverse
Mean pairwise identity 70.77
Shannon entropy 0.54608
G+C content 0.55508
Mean single sequence MFE -27.24
Consensus MFE -11.17
Energy contribution -11.79
Covariance contribution 0.62
Combinations/Pair 1.31
Mean z-score -1.47
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chrX 11659941 94 - 22422827
--CUGGUCUUCGGUCUGCAGUCCUCAGUUCCCCCCCUUUUGG-AUGGCCAAUGA-AGGCCAAUCGAAAUGGGAAAGCGAAUUCCACUUGGCCUGCAUC
--..((.(....).))((((.((..((((((.(((.((((((-.(((((.....-.))))).)))))).)))...).)))))......)).))))... ( -30.40, z-score =  -0.91, R)
>droPer1.super_28 412247 76 + 1111753
--------------CCGCAG----CAGCAGCCCCUCGGCCA---UGGCCAAUAA-AGGCCAAUCGAAAUGAGAAAGCGAAUUCCACCUGGUCCGCAUC
--------------..((.(----(....)).....(((((---(((((.....-.))))).(((...........)))........))))).))... ( -18.10, z-score =   0.11, R)
>dp4.chrXL_group1a 6887871 76 + 9151740
--------------CCGCAG----CAGCAGCCCCUCGGCCA---UGGCCAAUAA-AGGCCAAUCGAAAUGAGAAAGCGAAUUCCACCUGGUCCGCAUC
--------------..((.(----(....)).....(((((---(((((.....-.))))).(((...........)))........))))).))... ( -18.10, z-score =   0.11, R)
>droAna3.scaffold_13417 1408019 85 - 6960332
----------AUUCCCCCGAAUCUCGCUCGCCCCCGAUCCUCUCCAGCCUCCAAUCGGCCAAUCGAAAUGGGAAAGCGAAUUC---UUGGCCUGCAUC
----------....((..((((.(((((..(((.((((........(((.......)))..))))....)))..)))))))))---..))........ ( -19.30, z-score =  -0.13, R)
>droEre2.scaffold_4690 15208815 88 + 18748788
-------CCUCGGUCUGCAGUCUUCGAAUCCCCCCAUUUCGG--UGGCCAAUGA-AGGCCAAUCGAAAUGGGAAAGCGAAUUCCACUUGGCCUGCAUC
-------........(((((..((((......((((((((((--(((((.....-.)))).)))))))))))....))))..((....)).))))).. ( -33.40, z-score =  -2.91, R)
>droSec1.super_36 335545 95 - 449511
CUUCGGUCUUCGGUCUGCUGUCCUCAGUUCCCCCCAUUUCGA--UGGCCAAUGA-AGGCCAAUCGAAAUGGGAAAGCGAAUUCCACUUGGCCAGCAUC
....((.(....).))((((.((..((((((.((((((((((--(((((.....-.)))).)))))))))))...).)))))......)).))))... ( -36.80, z-score =  -3.50, R)
>droSim1.chrX 8976569 95 - 17042790
CUUCGGUCUUCGGUCUGUUGUCCUCAGUUCCCCCCAUUUCGA--UGGCCAAUGA-AGGCCAAUCGAAAUGGGAAAGCGAAUUCCACUUGGCCAGCAUC
....((((...((.(((.......)))..)).((((((((((--(((((.....-.)))).)))))))))))................))))...... ( -34.60, z-score =  -3.01, R)
>consensus
_______C_UCGGUCUGCAGUCCUCAGUUCCCCCCAUUUCG___UGGCCAAUGA_AGGCCAAUCGAAAUGGGAAAGCGAAUUCCACUUGGCCUGCAUC
................((((............(((.........(((((.......)))))........)))...((.((......)).))))))... (-11.17 = -11.79 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:35:25 2011