Locus 4334

Sequence ID	dm3.chr2R
Location	12,270,227 – 12,270,354
Length	127
Max. P	0.661244

overview

Window 2

Location	12,270,227 – 12,270,341
Length	114
Sequences	7
Columns	116
Reading direction	reverse
Mean pairwise identity	57.28
Shannon entropy	0.79326
G+C content	0.61924
Mean single sequence MFE	-26.26
Consensus MFE	-7.91
Energy contribution	-6.67
Covariance contribution	-1.24
Combinations/Pair	1.40
Mean z-score	-1.21
Structure conservation index	0.30
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.09
SVM RNA-class probability	0.537218
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12270227 114 - 21146708
ACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACUC--CCCAGCCACCUCCCCUGAUCUUUCCUGCACCGAACCACACCCCCCCCCCCCUUGGUUUGACCCU
....(((((((.((...))..))))))).(((((...((.((...)).))--..))))).......................(((((((...............)))))))..... ( -22.36, z-score =  -1.34, R)
>droSim1.chr2R 11002143 113 - 19596830
ACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACUC--CCCUGCCACCUCACCUGAUCUUUUCUGCAGCAAACCAC-CCCCCUCCCCCCCUGGAUUGACCCU
.((((((((((.((...))..)))))))..(((((..((..(((.((...--...)).))).))....((.....)).))))).......-.............)))......... ( -22.20, z-score =  -1.11, R)
>droSec1.super_1 9767887 107 - 14215200
ACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCCCUC--CCCUGCCACCUCACCUGAUC-UUUCUGCACCGAA------ACCCCCACCCCCUGGUUUGACCCU
((((.((((((.((...))..))))))((((.(((..(((((((......--...........)))..))))-.....))))))).------............))))........ ( -19.83, z-score =  -0.74, R)
>droYak2.chr2R 4424129 111 + 21139217
ACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGGCACCC--CCC-GCCACCCCCCCCUUUAAUCUUUUCAGGAACCCA--CCUCCUCCCGCCCUAGGUUGACUCU
(((.(((((((.((...))..))))))).(((.........(((((....--...-)))))...................((((.....--..))))...)))...)))....... ( -25.60, z-score =  -1.13, R)
>droAna3.scaffold_13266 15646043 93 - 19884421
ACCGAGGUGUUUGCCACGCUUGACACCUCGUCUGGG-CAUCCCUCCACCCCACCCGGAAGCC---CCUUACUCCUUCCUCCUGUCCCCCCGUGGGCU-------------------
..(((((((((.((...))..)))))))))...(((-(.(((.............))).)))---)................((((......)))).------------------- ( -28.02, z-score =  -1.80, R)
>dp4.chr3 15902166 86 + 19779522
AUCAAGGUGUUUGCCUCGGUUGACACCUCAUCAGGGUCGCCUCCCCGCACCGCUCUGGGGGCAGGCCCGAUCUCCGCCUCAGAUUG------------------------------
....(((((((.((....)).))))))).....(((((((((((..((...))...)))))).)))))(((((.......))))).------------------------------ ( -32.90, z-score =  -1.16, R)
>droPer1.super_2 4974469 86 + 9036312
AUCAAGGUGUUUGCCUCGGUUGACACCUCAUCAGGGUCGCCUCCCCGCACCGCUCUGGGGGCAGGCCCGAUCUCCGCCUCAGAUUG------------------------------
....(((((((.((....)).))))))).....(((((((((((..((...))...)))))).)))))(((((.......))))).------------------------------ ( -32.90, z-score =  -1.16, R)
>consensus
ACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACUC__CCCUGCCACCUCACCUGAUCUUUUCUUCAGCUAACC____CCCCUC_C_CC_U_G_UUGAC_CU
....(((((((..........))))))).............(((..............)))....................................................... ( -7.91 =  -6.67 +  -1.24)

alignment

secondary structure

dotplot

Window 3

Location	12,270,264 – 12,270,354
Length	90
Sequences	8
Columns	95
Reading direction	reverse
Mean pairwise identity	65.60
Shannon entropy	0.67330
G+C content	0.58708
Mean single sequence MFE	-27.12
Consensus MFE	-9.36
Energy contribution	-8.54
Covariance contribution	-0.83
Combinations/Pair	1.46
Mean z-score	-1.43
Structure conservation index	0.35
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.36
SVM RNA-class probability	0.661244
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12270264 90 - 21146708
---AGGGUUCGAUGUCACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACUCCC--CAGCCACCUCCCCUGAUCUUUCCUG
---((((.((((.((..((.(((((((.((...))..))))))).))..))))))..(((.(......--..).)))...))))........... ( -23.60, z-score =  -0.79, R)
>droSim1.chr2R 11002179 90 - 19596830
---AGGGUUCGAUGUCACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACUCCC--CUGCCACCUCACCUGAUCUUUUCUG
---.((((((((.((..((.(((((((.((...))..))))))).))..))))))..(((.((.....--.)).)))...))))........... ( -22.80, z-score =  -0.69, R)
>droSec1.super_1 9767918 89 - 14215200
---AGGGUUCGAUGUCACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCCCUCCC--CUGCCACCUCACCUGAUC-UUUCUG
---.((((((((.((..((.(((((((.((...))..))))))).))..))))))....)))).....--..................-...... ( -23.00, z-score =  -0.92, R)
>droYak2.chr2R 4424161 93 + 21139217
--AGGGGUUCGAUGUCACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGGCACCCCCCGCCACCCCCCCCUUUAAUCUUUUCAG
--(((((.((((.((..((.(((((((.((...))..))))))).))..))))))..(((((.......)))))...)))))............. ( -33.10, z-score =  -3.31, R)
>droEre2.scaffold_4845 8999449 79 + 22589142
--AGGGGUUCGAUGUCACCAAGGUGUUUGCAUCGCUUGACACCUCGGCUGGUCGAUUGUGGCACCCC---CAGAUAACCCCCCU-----------
--.((((((((((..((((.(((((((.((...))..))))))).)).)))))))(((.((....))---)))...)))))...----------- ( -26.80, z-score =  -0.71, R)
>droAna3.scaffold_13266 15646062 90 - 19884421
AGGGGUGUUCAAUGUCACCGAGGUGUUUGCCACGCUUGACACCUCGUCUGGG-CAUCCCUCCACCCCACCCGGAAGCCCCUUACUCCUUCC----
.((((((....(((((..(((((((((.((...))..)))))))))....))-))).....))))))....(((((..........)))))---- ( -34.70, z-score =  -3.06, R)
>dp4.chr3 15902194 74 + 19779522
AGGGGUGUUCGAUGUCAUCAAGGUGUUUGCCUCGGUUGACACCUCAUCAGGGUCGCCUCCCCGCACCGCUCUGG---------------------
((.(((((..((((......(((((((.((....)).))))))))))).(((......))).))))).))....--------------------- ( -26.50, z-score =  -0.98, R)
>droPer1.super_2 4974497 74 + 9036312
AGGGGUGUUCGAUGUCAUCAAGGUGUUUGCCUCGGUUGACACCUCAUCAGGGUCGCCUCCCCGCACCGCUCUGG---------------------
((.(((((..((((......(((((((.((....)).))))))))))).(((......))).))))).))....--------------------- ( -26.50, z-score =  -0.98, R)
>consensus
___GGGGUUCGAUGUCACCAAGGUGUUUGCAACGCUUGACACCUCGGCUGCUCGAUUGUGCCACCCCC__CUGCCACCCCCCCU_AUC_UU____
....((((............(((((((..........))))))).....((......))...))))............................. ( -9.36 =  -8.54 +  -0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:12 2011