Locus 3994

Sequence ID dm3.chr2R
Location 9,536,725 – 9,536,832
Length 107
Max. P 0.987845
window5464 window5465

overview

Window 4

Location 9,536,725 – 9,536,816
Length 91
Sequences 13
Columns 106
Reading direction forward
Mean pairwise identity 76.44
Shannon entropy 0.51372
G+C content 0.37339
Mean single sequence MFE -19.90
Consensus MFE -16.04
Energy contribution -16.39
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -1.13
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.954596
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9536725 91 + 21146708
--------------AGGUCCUUCAGUUGCCUCUUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------((((.........))))....-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -19.80, z-score =  -1.08, R)
>droSim1.chr2R 7982873 91 + 19596830
--------------AGGUCCUUCAGCUGCCUCUUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------((((.........))))....-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -19.80, z-score =  -0.83, R)
>droSec1.super_1 7063574 91 + 14215200
--------------AGGUCCUUCAGCUGCCUCUUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------((((.........))))....-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -19.80, z-score =  -0.83, R)
>droYak2.chr2R 13727710 91 - 21139217
--------------AGGUCCUUCAGCUGCCUCUUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------((((.........))))....-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -19.80, z-score =  -0.83, R)
>droEre2.scaffold_4845 6313119 91 - 22589142
--------------AGGUCCUUCAGCUGCCUCUUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------((((.........))))....-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -19.80, z-score =  -0.83, R)
>droAna3.scaffold_13266 16842822 91 + 19884421
--------------AGGUCCUUCAGCUCCCUCCUG-UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
--------------(((..............))).-..((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... ( -18.94, z-score =  -1.28, R)
>dp4.chr3 5231100 103 - 19779522
---AUGGACCCUUCAGUGCGCUCCUCCACUCUUUGGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
---......((...((((........))))....)).(((.(((((((((((((((....)))))......(((.....)))......)))))))))).))).... ( -22.10, z-score =  -1.15, R)
>droVir3.scaffold_12875 8134003 104 + 20611582
UGCACAUCUGUCUCUGU-UUCACACCCAUACACUG-CUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
.(((..........((.-....)).........))-)(((.(((((((((((((((....)))))......(((.....)))......)))))))))).))).... ( -19.31, z-score =  -0.74, R)
>droGri2.scaffold_15245 1615060 94 + 18325388
----------UGUCCAU-CUCUGACACACACACUG-CUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
----------((((...-....)))).........-.(((.(((((((((((((((....)))))......(((.....)))......)))))))))).))).... ( -20.90, z-score =  -1.92, R)
>droMoj3.scaffold_6496 7751470 81 - 26866924
------------------------GGCACACAUUG-CUGGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCACUCGAUAACAAUUUU
------------------------((((.....))-))...(((((((((((((((....)))))......(((.....)))......))))))))))........ ( -20.60, z-score =  -2.51, R)
>droWil1.scaffold_181009 1248593 90 + 3585778
---------CUCUCUGU-CCCUCGCCU-----CAG-UUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
---------........-.........-----...-.(((.(((((((((((((((....)))))......(((.....)))......)))))))))).))).... ( -19.40, z-score =  -2.40, R)
>droPer1.super_4 3056832 103 + 7162766
---AUGGACCCUUCAGUGCGCUCCUCCACUCUUUGGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
---......((...((((........))))....)).(((.(((((((((((((((....)))))......(((.....)))......)))))))))).))).... ( -22.10, z-score =  -1.15, R)
>triCas2.ChLG6 8385838 93 + 13544221
-----------GGGUGUUUCGAUUGUCGCUUGUUUGCGGCCACUUGAGUGUACGUU--UAAAAUUCGCAUUGAAACUUGUUCAAUAUUGAAAGCAACAUUAAUUUU
-----------.(((((((((((....((..(((((((..(((....)))..))).--..))))..))((((((.....)))))))))))....))))))...... ( -16.40, z-score =   0.81, R)
>consensus
______________AGGUCCUUCAGCUGCCUCUUG_UGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUU
......................................((.(((((((((((((((....)))))......(((.....)))......)))))))))).))..... (-16.04 = -16.39 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,536,739 – 9,536,832
Length 93
Sequences 13
Columns 116
Reading direction forward
Mean pairwise identity 81.05
Shannon entropy 0.36942
G+C content 0.33863
Mean single sequence MFE -18.56
Consensus MFE -16.04
Energy contribution -16.39
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -2.07
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.29
SVM RNA-class probability 0.987845
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9536739 93 + 21146708
----------CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCCA-------------
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).....................------------- ( -18.70, z-score =  -2.36, R)
>droSim1.chr2R 7982887 93 + 19596830
----------CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCCA-------------
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).....................------------- ( -18.70, z-score =  -2.36, R)
>droSec1.super_1 7063588 93 + 14215200
----------CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCCA-------------
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).....................------------- ( -18.70, z-score =  -2.36, R)
>droYak2.chr2R 13727724 93 - 21139217
----------CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCCA-------------
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).....................------------- ( -18.70, z-score =  -2.36, R)
>droEre2.scaffold_4845 6313133 93 - 22589142
----------CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCCA-------------
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).....................------------- ( -18.70, z-score =  -2.36, R)
>droAna3.scaffold_13266 16842836 106 + 19884421
----------CCUCCUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUUCCUUCAGCCCCCCUCCCA
----------.........((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).................................. ( -18.70, z-score =  -2.59, R)
>dp4.chr3 5231116 102 - 19779522
GCUCCUCCACUCUUUGGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUACAACAUUUUCUUCC--------------
......(((.....))).(((.(((((((((((((((....)))))......(((.....)))......)))))))))).)))...................-------------- ( -19.80, z-score =  -2.34, R)
>droVir3.scaffold_12875 8134030 89 + 20611582
----------UACACUGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAGUUUCU-----------------
----------........(((.(((((((((((((((....)))))......(((.....)))......)))))))))).)))................----------------- ( -19.30, z-score =  -1.85, R)
>droGri2.scaffold_15245 1615077 89 + 18325388
----------CACACUGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAGUCUCU-----------------
----------........(((.(((((((((((((((....)))))......(((.....)))......)))))))))).)))................----------------- ( -19.30, z-score =  -1.77, R)
>droMoj3.scaffold_6496 7751475 88 - 26866924
-----------ACAUUGCUGGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCACUCGAUAACAAUUUUAUAACAGUUUCU-----------------
-----------.....((((..(((((((((((((((....)))))......(((.....)))......))))))))))............))))....----------------- ( -18.64, z-score =  -1.76, R)
>droWil1.scaffold_181009 1248607 88 + 3585778
-----------CCUCAGUUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCU-----------------
-----------.......(((.(((((((((((((((....)))))......(((.....)))......)))))))))).)))................----------------- ( -19.40, z-score =  -2.71, R)
>droPer1.super_4 3056848 102 + 7162766
GCUCCUCCACUCUUUGGCUUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUACAACAUUUUCUUCC--------------
......(((.....))).(((.(((((((((((((((....)))))......(((.....)))......)))))))))).)))...................-------------- ( -19.80, z-score =  -2.34, R)
>triCas2.ChLG6 8385852 95 + 13544221
------UCGCUUGUUUGCGGCCACUUGAGUGUACGUU--UAAAAUUCGCAUUGAAACUUGUUCAAUAUUGAAAGCAACAUUAAUUUUCCCAUAUUUUCUCCCA-------------
------..((((....(((..(((....)))..))).--......(((.((((((.....))))))..)))))))............................------------- ( -12.90, z-score =   0.19, R)
>consensus
__________CCUCUUGUGUGAUAUUGAGUGCACUUUGUCAAAAGUUAUUUUGCAACAUUUGCUAUUAUGCGCUCGAUAACAAUUUUAUAACAUUUUCUCCC______________
...................((.(((((((((((((((....)))))......(((.....)))......)))))))))).)).................................. (-16.04 = -16.39 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:20:37 2011