Locus 226

Sequence ID	dm3.chr2L
Location	1,696,779 – 1,696,870
Length	91
Max. P	0.980124

overview

Window 8

Location	1,696,779 – 1,696,870
Length	91
Sequences	10
Columns	116
Reading direction	forward
Mean pairwise identity	75.64
Shannon entropy	0.45792
G+C content	0.53907
Mean single sequence MFE	-21.15
Consensus MFE	-12.07
Energy contribution	-11.86
Covariance contribution	-0.21
Combinations/Pair	1.20
Mean z-score	-2.25
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.04
SVM RNA-class probability	0.980124
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 1696779 91 + 23011544
----------ACCAGCCCCCCACAUAUAAUACCGCCCA---ACGAUACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAAUAGGAUGAGGAGAAAC----------
----------.........((.(((.......((....---.))....((((((..((((((.........))))))..)))).)--)......))).))......---------- ( -20.20, z-score =  -1.60, R)
>droSim1.chr2L 1706539 91 + 22036055
----------ACCAGCCCCCCACACAUAAUACCGCCCA---ACGAUACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAAUAGGAUGAGGAGAAAC----------
----------.......((.((..(.......((....---.))....((((((..((((((.........))))))..)))).)--)....)..)).))......---------- ( -20.60, z-score =  -1.67, R)
>droSec1.super_14 1631507 91 + 2068291
----------ACCAGCCCCCCACACAUUAUACCGCCCA---ACGAUACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAAUAGGAUGAGGAGAAAC----------
----------.........((.((..((((..((....---.))....((((((..((((((.........))))))..)))).)--).))))..)).))......---------- ( -20.70, z-score =  -1.63, R)
>droYak2.chr2L 1667213 91 + 22324452
----------ACCAGCCCCCCACACAUCAUACCGCCCA---ACGAGACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAAUAGGAUGAGGAGAAAC----------
----------.........((...((((....((....---.))....((((((..((((((.........))))))..)))).)--).....)))).))......---------- ( -21.40, z-score =  -1.43, R)
>droEre2.scaffold_4929 1740410 91 + 26641161
----------ACCAGCCCCCCACACAUAAUACCGCCCA---ACGAGACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAAUAGGAUGAGGAGAAAC----------
----------.......((.((..(.......((....---.))....((((((..((((((.........))))))..)))).)--)....)..)).))......---------- ( -20.60, z-score =  -1.51, R)
>droAna3.scaffold_12916 15094999 91 + 16180835
----------ACCAGCCCACAACAACACAUAAUACCGCCCAACGAGACGCCCGCUUUGACCUCCACGCCCAAGGUCAAUGUGGAG--CAGUAGGAGGAGCCAC-------------
----------..........................((((..(...((((((((.(((((((.........))))))).)))).)--).)).)..)).))...------------- ( -23.00, z-score =  -1.78, R)
>dp4.chr4_group2 754394 91 - 1235136
----------ACCAACCCCCCCCACACUAUACCGCCCA---ACGAUACGCCUACAUUGACCUCCACGCCCAAGGUCAAUGUAGAG--CAGUAAGAAGGAGAGAAGC----------
----------.........................((.---.(..(((((((((((((((((.........)))))))))))).)--).))).)..))........---------- ( -23.00, z-score =  -4.87, R)
>droPer1.super_8 3402604 91 + 3966273
----------ACCAACCCCCCCCACACUAUACCGCCCA---ACGAUACGCCUACAUUGACCUCCACGCCCAAGGUCAAUGUAGAG--CAGUAAGAAGGAGAGAAGC----------
----------.........................((.---.(..(((((((((((((((((.........)))))))))))).)--).))).)..))........---------- ( -23.00, z-score =  -4.87, R)
>droWil1.scaffold_180708 3578099 105 + 12563649
AGCCAAUAUAACCAGCCCUCAAUAUAAUAUACCGCCCAAUCAUGAGAUGCCCACAUUGACCUCAACGCCCAAGAUCAAUGUGGAA--CAGCAAUAAAUUGAAAAAGU---------
.((...........((.((((.....................))))..))(((((((((.((.........)).)))))))))..--..))................--------- ( -15.90, z-score =  -1.71, R)
>droGri2.scaffold_15252 10882241 103 + 17193109
----------ACCAGCCCCAUGAUGAUGAUUAUGCCAC---ACGAACCACCCACAUUGACCUCAACGCCCAAGCUCAAUGUGGAUGUCAGUGAGCAGUAAGCAAAUGAUGAUGAAA
----------........(((.((.((..(((((((((---..((..((.(((((((((.((.........)).))))))))).)))).))).))).)))....)).)).)))... ( -23.10, z-score =  -1.49, R)
>consensus
__________ACCAGCCCCCCACACAUUAUACCGCCCA___ACGAUACGCCCACUCUGACCUCCACGCCCAAGGUCAAUGUGGAG__CAAUAGGAUGAGGAGAAAC__________
..................................................((((..((((((.........))))))..))))................................. (-12.07 = -11.86 +  -0.21)

alignment

secondary structure

dotplot

Window 9

Location	1,696,779 – 1,696,870
Length	91
Sequences	10
Columns	116
Reading direction	reverse
Mean pairwise identity	75.64
Shannon entropy	0.45792
G+C content	0.53907
Mean single sequence MFE	-35.32
Consensus MFE	-18.57
Energy contribution	-17.96
Covariance contribution	-0.61
Combinations/Pair	1.68
Mean z-score	-2.06
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.42
SVM RNA-class probability	0.938136
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 1696779 91 - 23011544
----------GUUUCUCCUCAUCCUAUUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAGAGUGGGCGUAUCGU---UGGGCGGUAUUAUAUGUGGGGGGCUGGU----------
----------....((((((((......(--(.((((.((((((((.......)))))))).))))))((((((.---....)))))).....)))))))).....---------- ( -33.70, z-score =  -1.39, R)
>droSim1.chr2L 1706539 91 - 22036055
----------GUUUCUCCUCAUCCUAUUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAGAGUGGGCGUAUCGU---UGGGCGGUAUUAUGUGUGGGGGGCUGGU----------
----------....(((((((..(....(--(.((((.((((((((.......)))))))).))))))((((((.---....))))))...)..))))))).....---------- ( -34.20, z-score =  -1.37, R)
>droSec1.super_14 1631507 91 - 2068291
----------GUUUCUCCUCAUCCUAUUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAGAGUGGGCGUAUCGU---UGGGCGGUAUAAUGUGUGGGGGGCUGGU----------
----------....(((((((..(....(--(.((((.((((((((.......)))))))).))))))((((((.---....))))))...)..))))))).....---------- ( -34.80, z-score =  -1.58, R)
>droYak2.chr2L 1667213 91 - 22324452
----------GUUUCUCCUCAUCCUAUUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAGAGUGGGCGUCUCGU---UGGGCGGUAUGAUGUGUGGGGGGCUGGU----------
----------((..((((.((((.(((((--((((((.((((((((.......)))))))).)))((((...)))---))))))))).)))).).)))..))....---------- ( -36.40, z-score =  -1.50, R)
>droEre2.scaffold_4929 1740410 91 - 26641161
----------GUUUCUCCUCAUCCUAUUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAGAGUGGGCGUCUCGU---UGGGCGGUAUUAUGUGUGGGGGGCUGGU----------
----------....(((((((..(((.((--((((((.((((((((.......)))))))).)))))(((((...---.)))))))).)).)..))))))).....---------- ( -33.00, z-score =  -0.78, R)
>droAna3.scaffold_12916 15094999 91 - 16180835
-------------GUGGCUCCUCCUACUG--CUCCACAUUGACCUUGGGCGUGGAGGUCAAAGCGGGCGUCUCGUUGGGCGGUAUUAUGUGUUGUUGUGGGCUGGU----------
-------------......((.(((((.(--(..(((((..(((((.((((.(((.(((......))).))))))).)).)))...)))))..)).)))))..)).---------- ( -31.30, z-score =  -0.12, R)
>dp4.chr4_group2 754394 91 + 1235136
----------GCUUCUCUCCUUCUUACUG--CUCUACAUUGACCUUGGGCGUGGAGGUCAAUGUAGGCGUAUCGU---UGGGCGGUAUAGUGUGGGGGGGGUUGGU----------
----------(((..((((((((.(((((--(.(((((((((((((.......)))))))))))))))((((((.---....)))))))))).))))))))..)))---------- ( -42.20, z-score =  -4.84, R)
>droPer1.super_8 3402604 91 - 3966273
----------GCUUCUCUCCUUCUUACUG--CUCUACAUUGACCUUGGGCGUGGAGGUCAAUGUAGGCGUAUCGU---UGGGCGGUAUAGUGUGGGGGGGGUUGGU----------
----------(((..((((((((.(((((--(.(((((((((((((.......)))))))))))))))((((((.---....)))))))))).))))))))..)))---------- ( -42.20, z-score =  -4.84, R)
>droWil1.scaffold_180708 3578099 105 - 12563649
---------ACUUUUUCAAUUUAUUGCUG--UUCCACAUUGAUCUUGGGCGUUGAGGUCAAUGUGGGCAUCUCAUGAUUGGGCGGUAUAUUAUAUUGAGGGCUGGUUAUAUUGGCU
---------.....((((((.((.(((((--((((((((((((((..(...)..))))))))))))..(((....)))..)))))))...)).))))))(((..((...))..))) ( -33.30, z-score =  -3.05, R)
>droGri2.scaffold_15252 10882241 103 - 17193109
UUUCAUCAUCAUUUGCUUACUGCUCACUGACAUCCACAUUGAGCUUGGGCGUUGAGGUCAAUGUGGGUGGUUCGU---GUGGCAUAAUCAUCAUCAUGGGGCUGGU----------
(..(((.((....((.(((.(((((((.((((((((((((((.((..(...)..)).))))))))))).))).))---).))))))).))..)).)))..).....---------- ( -32.10, z-score =  -1.15, R)
>consensus
__________GUUUCUCCUCAUCCUACUG__CUCCACAUUGACCUUGGGCGUGGAGGUCAAAGUGGGCGUAUCGU___UGGGCGGUAUAAUGUGUGGGGGGCUGGU__________
.............((((((..............((((.((((((((.......)))))))).))))((.((.......)).))............))))))............... (-18.57 = -17.96 +  -0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:08:57 2011