Locus 717

Sequence ID dm3.chr2L
Location 5,068,563 – 5,068,698
Length 135
Max. P 0.986272
window950 window951 window952 window953

overview

Window 0

Location 5,068,563 – 5,068,661
Length 98
Sequences 9
Columns 108
Reading direction forward
Mean pairwise identity 69.64
Shannon entropy 0.59290
G+C content 0.46931
Mean single sequence MFE -29.80
Consensus MFE -14.48
Energy contribution -14.33
Covariance contribution -0.14
Combinations/Pair 1.38
Mean z-score -1.99
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.23
SVM RNA-class probability 0.986272
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5068563 98 + 23011544
----UAUACAUGUAUGAUCACAUUGGCUUGUGGGCGUGGCACUU-CAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCC-CGCCGAU---
----..............((((......))))((((.((((.((-(((((((((((.((((.((.....)).)))))))-).)).))))))).))))-))))...--- ( -39.30, z-score =  -3.61, R)
>droSec1.super_5 3155472 96 + 5866729
-----AUACAUGUAUGAUC-CAUUGGCUUGUGGGCGUGGCACUU-CGAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCC-CGCCAAU---
-----.((((.((......-.....)).))))((((.((((.((-(((((((((((.((((.((.....)).)))))))-).)).))))))).))))-))))...--- ( -36.80, z-score =  -2.69, R)
>droYak2.chr2L 11868077 95 - 22324452
------UAUAC-UAUAAUC--AUUGGCUUGUGGGCGUGGCACUU-CAAUUGGUCUGACUUUGCCCGACUGGAAAAGCGG-CACCUAAUUGAAAUGCC-CGCCACAAU-
------.....-.......--......((((((.((.((((.((-(((((((((((.((((.((.....)).)))))))-.))).))))))).))))-)))))))).- ( -34.50, z-score =  -3.77, R)
>droEre2.scaffold_4929 5148425 91 + 26641161
---------UU-UAUGAUC-CAUUGGCUUGUGGGCGUGGCACUU-CAAUUGGUCUGACUUUGCCCGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCC-CGCCAAA---
---------..-.......-(((......)))((((.((((.((-(((((((((((.((((.((.....)).)))))))-.))).))))))).))))-))))...--- ( -33.00, z-score =  -2.12, R)
>droAna3.scaffold_12916 13706195 93 + 16180835
---------CUCCGUGUAUACAUAUG-UUGUGGGCGUGGCACUU-CAAUUGGUCUAACUUUCCCGGAAUGGUAAAGCAGUCACUUAAUUGAAAUGCC-CGCCAAU---
---------.........((((....-.))))((((.((((.((-((((((((....((((.((.....)).)))).....)).)))))))).))))-))))...--- ( -26.60, z-score =  -1.66, R)
>dp4.chr4_group4 1588268 85 + 6586962
--------------UGUGCGCAUUGG-GUUGGGGCGUGGCACUU-CAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUGCAACU-AAUUGAAAUGUC-CGCCAAU---
--------------.(((.(((((.(-(((((((((.(((.((.-......)).--))).)))))((((.....)))).)))))-......))))).-)))....--- ( -26.30, z-score =   0.13, R)
>droPer1.super_10 591774 85 + 3432795
--------------UGUGCGCAUUGG-GUUGGGGCGUGGCACUU-CAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUGCAACU-AAUUGAAAUGUC-CGCCAAU---
--------------.(((.(((((.(-(((((((((.(((.((.-......)).--))).)))))((((.....)))).)))))-......))))).-)))....--- ( -26.30, z-score =   0.13, R)
>droWil1.scaffold_180703 1359543 88 + 3946847
--------------UUCACACAUUCGUUUUUGUCUAUGGUAUUUUCAAUUUGGCU-CCUUUAUCUGGCUGAAAAAGCUG-CAACUAAUUGAAAUGCC-CAUUUAA---
--------------.......................(((((((.(((((..((.-.((((.((.....)).))))..)-)....))))))))))))-.......--- ( -16.30, z-score =  -1.33, R)
>droGri2.scaffold_15252 11801610 107 + 17193109
UCUCUAUCUCUGUAUCUCUCUCUCUGGUUGAGGGCGUUCCAUUU-CAAUUUGGCGCUUUUUGUCUGGCUGGAAAAGCUGCACAUUAAUUGAAAUGUCGCGUCGUUAAU
..........................(((((.(((((..(((((-((((((((((((((((.........))))))).)).))..))))))))))..))))).))))) ( -29.10, z-score =  -2.99, R)
>consensus
__________U_UAUGAUC_CAUUGGCUUGUGGGCGUGGCACUU_CAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG_CACCUAAUUGAAAUGCC_CGCCAAU___
................................((((.((((.((.(((((.......((((.((.....)).)))).........))))))).)))).))))...... (-14.48 = -14.33 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,068,563 – 5,068,661
Length 98
Sequences 9
Columns 108
Reading direction reverse
Mean pairwise identity 69.64
Shannon entropy 0.59290
G+C content 0.46931
Mean single sequence MFE -27.67
Consensus MFE -11.59
Energy contribution -12.21
Covariance contribution 0.62
Combinations/Pair 1.23
Mean z-score -2.32
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.20
SVM RNA-class probability 0.985515
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5068563 98 - 23011544
---AUCGGCG-GGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUG-AAGUGCCACGCCCACAAGCCAAUGUGAUCAUACAUGUAUA----
---...((((-((((((((((((.(((.-..(((((.((.....)).)))))..))).)))))-))))))).))))((((......))))..............---- ( -38.10, z-score =  -4.47, R)
>droSec1.super_5 3155472 96 - 5866729
---AUUGGCG-GGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUCG-AAGUGCCACGCCCACAAGCCAAUG-GAUCAUACAUGUAU-----
---...((((-((((((((.(((.(((.-..(((((.((.....)).)))))..))).))).)-))))))).)))).........(((-.......)))....----- ( -31.20, z-score =  -2.19, R)
>droYak2.chr2L 11868077 95 + 22324452
-AUUGUGGCG-GGCAUUUCAAUUAGGUG-CCGCUUUUCCAGUCGGGCAAAGUCAGACCAAUUG-AAGUGCCACGCCCACAAGCCAAU--GAUUAUA-GUAUA------
-.((((((((-((((((((((((.(((.-..((((((((....))).)))))...))))))))-))))))).)).))))))......--.......-.....------ ( -36.80, z-score =  -4.28, R)
>droEre2.scaffold_4929 5148425 91 - 26641161
---UUUGGCG-GGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCGGGCAAAGUCAGACCAAUUG-AAGUGCCACGCCCACAAGCCAAUG-GAUCAUA-AA---------
---...((((-((((((((((((.(((.-..((((((((....))).)))))...))))))))-))))))).))))............-.......-..--------- ( -33.50, z-score =  -2.87, R)
>droAna3.scaffold_12916 13706195 93 - 16180835
---AUUGGCG-GGCAUUUCAAUUAAGUGACUGCUUUACCAUUCCGGGAAAGUUAGACCAAUUG-AAGUGCCACGCCCACAA-CAUAUGUAUACACGGAG---------
---...((((-((((((((((((..((....(((((.((.....)).)))))...)).)))))-))))))).)))).....-.................--------- ( -28.70, z-score =  -3.06, R)
>dp4.chr4_group4 1588268 85 - 6586962
---AUUGGCG-GACAUUUCAAUU-AGUUGCAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUG-AAGUGCCACGCCCCAAC-CCAAUGCGCACA--------------
---...((((-(.((((((((((-.......(((.....)))..(((.....--))).)))))-))))).).)))).....-............-------------- ( -22.80, z-score =  -0.80, R)
>droPer1.super_10 591774 85 - 3432795
---AUUGGCG-GACAUUUCAAUU-AGUUGCAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUG-AAGUGCCACGCCCCAAC-CCAAUGCGCACA--------------
---...((((-(.((((((((((-.......(((.....)))..(((.....--))).)))))-))))).).)))).....-............-------------- ( -22.80, z-score =  -0.80, R)
>droWil1.scaffold_180703 1359543 88 - 3946847
---UUAAAUG-GGCAUUUCAAUUAGUUG-CAGCUUUUUCAGCCAGAUAAAGG-AGCCAAAUUGAAAAUACCAUAGACAAAAACGAAUGUGUGAA--------------
---....(((-(...((((((((....(-(..((((.((.....)).)))).-.))..))))))))...)))).....................-------------- ( -14.00, z-score =  -0.03, R)
>droGri2.scaffold_15252 11801610 107 - 17193109
AUUAACGACGCGACAUUUCAAUUAAUGUGCAGCUUUUCCAGCCAGACAAAAAGCGCCAAAUUG-AAAUGGAACGCCCUCAACCAGAGAGAGAGAUACAGAGAUAGAGA
.........(((.((((((((((..((.((.((((((...........)))))))))))))))-)))))...))).(((.....)))..................... ( -21.10, z-score =  -2.40, R)
>consensus
___AUUGGCG_GGCAUUUCAAUUAGGUG_CAGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUG_AAGUGCCACGCCCACAAGCCAAUG_GAACAUA_A__________
......((((.(.((((((((((........(((((.((.....)).)))))......))))).))))).).))))................................ (-11.59 = -12.21 +   0.62)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,068,593 – 5,068,698
Length 105
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 71.30
Shannon entropy 0.56587
G+C content 0.47898
Mean single sequence MFE -26.69
Consensus MFE -16.17
Energy contribution -16.30
Covariance contribution 0.13
Combinations/Pair 1.14
Mean z-score -1.27
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945579
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5068593 105 + 23011544
CGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCG--AUCAGUGCUCGAUUACGAUCGACACAAGCGACAUUUUCG
(((((((.(((((((((((((.((((.((.....)).)))))))-).)).))))))).)))).....--....(((.(((((....))))))))..)))......... ( -36.00, z-score =  -2.64, R)
>droSec1.super_5 3155500 79 + 5866729
CGUGGCACUUCGAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCA--AUCGACAUUUUCG--------------------------
((.((((.(((((((((((((.((((.((.....)).)))))))-).)).))))))).))))))...--.............-------------------------- ( -27.50, z-score =  -2.54, R)
>droYak2.chr2L 11868102 107 - 22324452
CGUGGCACUUCAAUUGGUCUGACUUUGCCCGACUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCACAAUCAGUGCUCGAUCGUGAUCGACACAAGCGACAUUUUCG
(((((((.(((((((((((((.((((.((.....)).)))))))-.))).))))))).))))...........(((.(((((....))))))))..)))......... ( -33.40, z-score =  -2.16, R)
>droEre2.scaffold_4929 5148448 105 + 26641161
CGUGGCACUUCAAUUGGUCUGACUUUGCCCGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCA--AACAGUGCUCGACCAUGAUCGGCACAAGCGACAUUUUCG
(((((((.(((((((((((((.((((.((.....)).)))))))-.))).))))))).)))).....--....((((.(((......)))))))..)))......... ( -33.50, z-score =  -1.60, R)
>droAna3.scaffold_12916 13706219 89 + 16180835
CGUGGCACUUCAAUUGGUCUAACUUUCCCGGAAUGGUAAAGCAGUCACUUAAUUGAAAUGCCCGCCA--AUCA----CGAGCAACAUUUUUUUCG-------------
.(.((((.((((((((((....((((.((.....)).)))).....)).)))))))).)))))(((.--....----.).)).............------------- ( -17.40, z-score =  -0.37, R)
>dp4.chr4_group4 1588287 101 + 6586962
CGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCA--AUCAAU--UAAGCAAUAAACAACAUAAGCAACACUUUCG
.((((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)).))))..--......--............................... ( -19.50, z-score =   0.16, R)
>droPer1.super_10 591793 101 + 3432795
CGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCA--AUCAAU--UAAGCAAUAAACAACAUAAGCAACAAUUUCA
.((((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)).))))..--......--............................... ( -19.50, z-score =   0.27, R)
>consensus
CGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG_CACCUAAUUGAAAUGCCCGCCA__AUCAAU__UCAACAAUAAUCGACACAAGCGACAUUUUCG
((.((((.(((((((((.....((((.((.....)).)))).......))))))))).))))))............................................ (-16.17 = -16.30 +   0.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,068,593 – 5,068,698
Length 105
Sequences 7
Columns 108
Reading direction reverse
Mean pairwise identity 71.30
Shannon entropy 0.56587
G+C content 0.47898
Mean single sequence MFE -31.39
Consensus MFE -17.07
Energy contribution -17.73
Covariance contribution 0.65
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976737
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5068593 105 - 23011544
CGAAAAUGUCGCUUGUGUCGAUCGUAAUCGAGCACUGAU--CGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUGAAGUGCCACG
......(((((...((((((((....))))).)))....--)))))((((((((((((.(((.-..(((((.((.....)).)))))..))).))))))))))))... ( -39.40, z-score =  -3.22, R)
>droSec1.super_5 3155500 79 - 5866729
--------------------------CGAAAAUGUCGAU--UGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUCGAAGUGCCACG
--------------------------......((((...--.))))((((((((.(((.(((.-..(((((.((.....)).)))))..))).))).))))))))... ( -24.80, z-score =  -1.57, R)
>droYak2.chr2L 11868102 107 + 22324452
CGAAAAUGUCGCUUGUGUCGAUCACGAUCGAGCACUGAUUGUGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGUCGGGCAAAGUCAGACCAAUUGAAGUGCCACG
......((((((..((((((((....))))).))).....))))))((((((((((((.(((.-..((((((((....))).)))))...)))))))))))))))... ( -40.00, z-score =  -2.74, R)
>droEre2.scaffold_4929 5148448 105 - 26641161
CGAAAAUGUCGCUUGUGCCGAUCAUGGUCGAGCACUGUU--UGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCGGGCAAAGUCAGACCAAUUGAAGUGCCACG
.........((((.((((((((....)))).))))....--.))))((((((((((((.(((.-..((((((((....))).)))))...)))))))))))))))... ( -41.30, z-score =  -2.85, R)
>droAna3.scaffold_12916 13706219 89 - 16180835
-------------CGAAAAAAAUGUUGCUCG----UGAU--UGGCGGGCAUUUCAAUUAAGUGACUGCUUUACCAUUCCGGGAAAGUUAGACCAAUUGAAGUGCCACG
-------------((..((..(((.....))----)..)--)..))((((((((((((..((....(((((.((.....)).)))))...)).))))))))))))... ( -22.90, z-score =  -1.15, R)
>dp4.chr4_group4 1588287 101 - 6586962
CGAAAGUGUUGCUUAUGUUGUUUAUUGCUUA--AUUGAU--UGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACG
.....(((..((((..(((((.....(((((--((((((--(((........)))))))))))-.)))....)))))..(((.....--)))......))))..))). ( -27.20, z-score =  -0.83, R)
>droPer1.super_10 591793 101 - 3432795
UGAAAUUGUUGCUUAUGUUGUUUAUUGCUUA--AUUGAU--UGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACG
........((((((..(((((.....(((((--((((((--(((........)))))))))))-.)))....))))).)))))).((--((.........)))).... ( -24.10, z-score =   0.02, R)
>consensus
CGAAAAUGUCGCUUGUGUCGAUCAUUGCCGA__ACUGAU__UGGCGGGCAUUUCAAUUAGGUG_CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUGAAGUGCCACG
............................................((((((((((((((.(......(((((.((.....)).)))))....).)))))))))))).)) (-17.07 = -17.73 +   0.65)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:17:57 2011