Locus 13550

Sequence ID dm3.chrX
Location 7,337,842 – 7,337,976
Length 134
Max. P 0.988343
window18654 window18655

overview

Window 4

Location 7,337,842 – 7,337,976
Length 134
Sequences 6
Columns 157
Reading direction forward
Mean pairwise identity 68.10
Shannon entropy 0.57215
G+C content 0.44280
Mean single sequence MFE -36.27
Consensus MFE -16.57
Energy contribution -16.99
Covariance contribution 0.42
Combinations/Pair 1.28
Mean z-score -2.28
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.32
SVM RNA-class probability 0.988343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7337842 134 + 22422827
-----------GCAAUUCGCUGCUAUUUA-UUGCUCCUGCCGAUAAUUUCCACAUUAGGCUGAC-UAUU-UGUAUAUCUAAUACGAUGCAUCAAUGCAUCAACCUGUCUCCCGUUUCGGAGAUGCAAGAUGCAUUUCCUUCUAGUGGA---------
-----------(((......)))...(((-((((....).))))))..(((((....((..(((-....-.((((.....))))((((((....)))))).....)))..)).....((((((((.....)))))))).....)))))--------- ( -38.10, z-score =  -3.28, R)
>droAna3.scaffold_13117 184564 125 + 5790199
---------------------GGGAUUCGGUGACUACUUCCCGGGAGUCUCG---GGAGCUGUC-------CCCUAUCUCUUCCGAUGUAUCGAUGCGUCCACCUGUCUCCCGUUUGGGAAA-GCCAGCUGUCCCCUCGGACAGGUCUCCCAGCGAA
---------------------((((...((.(((...((((((((...))))---))))..)))-------.))..........((((((....)))))).((((((...(((...((((.(-(....)).))))..))))))))).))))...... ( -45.30, z-score =  -0.44, R)
>droEre2.scaffold_4690 16249336 144 + 18748788
----GUAAUUCUUAGCUAUUUGCGCCACUAUUUCUCCUGCCGAUAAUUUCCACAUAAGGCUGACCUAUUGCAUAUAUCUAAAACGAUGCAUCAAUGCAUCCACCUGUCCCCCGAUUCGGAGAUGCAAGAUGCAUUUUCUGCUACUGGA---------
----(((....((((.(((.((((....((..((....(((................))).))..)).)))).))).))))...((((((((..((((((..(..(((....)))..)..)))))).))))))))...))).......--------- ( -28.39, z-score =  -0.41, R)
>droYak2.chrX 7764441 125 - 21770863
---------------------GCAAUUUAGUUUCGCCUGCCGAUAAUUUCCACAUAAGGCUGAC-UAUU-GGUAUAUCUAGUACGAUGCAUCAAUGCAUCCACCUGUCCCCCAAUUCGGCGAUGCAAGAUGCAUUUCCUUCUACUGCA---------
---------------------(((.(((.((.(((((((((((((.((.((......))..)).-))))-))))....(((...((((((....))))))...)))...........))))).)).))))))................--------- ( -30.60, z-score =  -1.85, R)
>droSec1.super_24 547099 145 + 912625
ACAAUUCGCAGCU-AUUUAUUGCUCCAUUAUUUCUGCUGCCGAUAAUUUCCACAUAAGGUUGAC-UAUU-UGUAUAUCUAAUACGAUGCAUCAAUGCAUCAACCUGUCUCCCAAUUCGGAGAUGCAAGAUGCAUUUCCUUCUAGUGGA---------
...(((.(((((.-.....................))))).)))....(((((....((..(((-....-.((((.....))))((((((....)))))).....)))..)).....((((((((.....)))))))).....)))))--------- ( -41.65, z-score =  -4.20, R)
>droSim1.chrX 5865064 139 + 17042790
-------GCAAUUUAUUUAUUGCUCCAUUAUUUCUCCUGCCGAUAAUUUCCACAUAAGGCUGAC-UAUU-UGUAUAUCUAAUACGAUGCAUCAAUGCAUCAACCUGUCUCCCAAUUCGGAGAUGCAAGAUGCAUUUCCUUCUAGUGUA---------
-------(((((......)))))...........................(((....((..(((-....-.((((.....))))((((((....)))))).....)))..)).....((((((((.....)))))))).....)))..--------- ( -33.60, z-score =  -3.47, R)
>consensus
____________U_AUU__UUGCUACAUUAUUUCUCCUGCCGAUAAUUUCCACAUAAGGCUGAC_UAUU_UGUAUAUCUAAUACGAUGCAUCAAUGCAUCAACCUGUCUCCCAAUUCGGAGAUGCAAGAUGCAUUUCCUUCUAGUGGA_________
....................................(.(((................))).)......................((((((....)))))).................((((((((.....))))))))................... (-16.57 = -16.99 +   0.42)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,337,842 – 7,337,976
Length 134
Sequences 6
Columns 157
Reading direction reverse
Mean pairwise identity 68.10
Shannon entropy 0.57215
G+C content 0.44280
Mean single sequence MFE -38.98
Consensus MFE -16.98
Energy contribution -18.10
Covariance contribution 1.12
Combinations/Pair 1.25
Mean z-score -1.55
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.804042
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7337842 134 - 22422827
---------UCCACUAGAAGGAAAUGCAUCUUGCAUCUCCGAAACGGGAGACAGGUUGAUGCAUUGAUGCAUCGUAUUAGAUAUACA-AAUA-GUCAGCCUAAUGUGGAAAUUAUCGGCAGGAGCAA-UAAAUAGCAGCGAAUUGC-----------
---------(((.......)))..(((.((((((.(((((......))))).(((((((((((....)))...((((.....)))).-....-))))))))................))))))))).-......((((....))))----------- ( -35.70, z-score =  -1.66, R)
>droAna3.scaffold_13117 184564 125 - 5790199
UUCGCUGGGAGACCUGUCCGAGGGGACAGCUGGC-UUUCCCAAACGGGAGACAGGUGGACGCAUCGAUACAUCGGAAGAGAUAGGG-------GACAGCUCC---CGAGACUCCCGGGAAGUAGUCACCGAAUCCC---------------------
......((((..((((((((((.(..((.(((..-((((((....))))))))).))..).).))).....((....)))))))).-------(((.(((((---((.......)))).))).)))......))))--------------------- ( -48.60, z-score =  -1.03, R)
>droEre2.scaffold_4690 16249336 144 - 18748788
---------UCCAGUAGCAGAAAAUGCAUCUUGCAUCUCCGAAUCGGGGGACAGGUGGAUGCAUUGAUGCAUCGUUUUAGAUAUAUGCAAUAGGUCAGCCUUAUGUGGAAAUUAUCGGCAGGAGAAAUAGUGGCGCAAAUAGCUAAGAAUUAC----
---------.......(((...(((((((((....(((((......))))).....)))))))))..)))....((((((.(((.(((...(((....)))..(((.((.....)).)))..............))).))).)))))).....---- ( -37.30, z-score =  -0.56, R)
>droYak2.chrX 7764441 125 + 21770863
---------UGCAGUAGAAGGAAAUGCAUCUUGCAUCGCCGAAUUGGGGGACAGGUGGAUGCAUUGAUGCAUCGUACUAGAUAUACC-AAUA-GUCAGCCUUAUGUGGAAAUUAUCGGCAGGCGAAACUAAAUUGC---------------------
---------.(((((....((....(((((.(((((((((......(....).))).))))))..)))))(((......)))...))-..((-((..((((...((.((.....)).))))))...)))).)))))--------------------- ( -36.90, z-score =  -1.74, R)
>droSec1.super_24 547099 145 - 912625
---------UCCACUAGAAGGAAAUGCAUCUUGCAUCUCCGAAUUGGGAGACAGGUUGAUGCAUUGAUGCAUCGUAUUAGAUAUACA-AAUA-GUCAACCUUAUGUGGAAAUUAUCGGCAGCAGAAAUAAUGGAGCAAUAAAU-AGCUGCGAAUUGU
---------(((((...((((..(((((((.((((((.((......(....).))..))))))..))))))).((((.....)))).-....-.....))))..)))))........(((((.....................-.)))))....... ( -41.65, z-score =  -2.64, R)
>droSim1.chrX 5865064 139 - 17042790
---------UACACUAGAAGGAAAUGCAUCUUGCAUCUCCGAAUUGGGAGACAGGUUGAUGCAUUGAUGCAUCGUAUUAGAUAUACA-AAUA-GUCAGCCUUAUGUGGAAAUUAUCGGCAGGAGAAAUAAUGGAGCAAUAAAUAAAUUGC-------
---------..(((...((((..(((((((.((((((.((......(....).))..))))))..))))))).((((.....)))).-....-.....))))..)))...........((..(....)..))..(((((......)))))------- ( -33.70, z-score =  -1.65, R)
>consensus
_________UCCACUAGAAGGAAAUGCAUCUUGCAUCUCCGAAUCGGGAGACAGGUGGAUGCAUUGAUGCAUCGUAUUAGAUAUACA_AAUA_GUCAGCCUUAUGUGGAAAUUAUCGGCAGGAGAAAUAAAAGAGCAA__AAU_A____________
......................((((((((..((.(((((......)))))...)).))))))))..((((((......))).................((..(((.((.....)).)))..))..........))).................... (-16.98 = -18.10 +   1.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:23:27 2011