Locus 4936

Sequence ID	dm3.chr2R
Location	16,545,375 – 16,545,472
Length	97
Max. P	0.884213

overview

Window 6

Location	16,545,375 – 16,545,472
Length	97
Sequences	11
Columns	105
Reading direction	forward
Mean pairwise identity	80.94
Shannon entropy	0.42218
G+C content	0.54223
Mean single sequence MFE	-29.73
Consensus MFE	-26.77
Energy contribution	-26.61
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-0.93
Structure conservation index	0.90
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.00
SVM RNA-class probability	0.871871
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16545375 97 + 21146708
---AGGCAGUGGGAUUUUCAAUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAGAGGU-----
---..((..(((..((.......))..)))..))((.......))((.(((((((((.((((....))))(((((.......))))).))))))))).))----- ( -31.50, z-score =  -0.85, R)
>droSim1.chr2R 15207185 97 + 19596830
---AGCCAGUGGGAUUCUCAAUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAGAGGU-----
---.((((...(((.((......)).))).))))((.......))((.(((((((((.((((....))))(((((.......))))).))))))))).))----- ( -35.30, z-score =  -1.66, R)
>droSec1.super_1 14099502 85 + 14215200
---------------AGCCAGUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAGAGUU-----
---------------.(((.((((.(.(....).))))))))...((.(((((((((.((((....))))(((((.......))))).))))))))))).----- ( -28.40, z-score =  -0.88, R)
>droYak2.chr2R 8488821 94 - 21139217
---AGGCGGUGCAAUUCUCAAUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAAA--------
---..((((.(((((.....)))).).)))).((((.......))))...(((((((.((((....))))(((((.......))))).)))))))..-------- ( -30.60, z-score =  -0.93, R)
>droEre2.scaffold_4845 10693280 102 + 22589142
---AGGCAGUGGAAUCUUCAAUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAAAAAGUUGAU
---((((...(((.((.......)).)))...((((.......))))))))((((((.((((....))))(((((.......))))).))))))........... ( -30.20, z-score =  -0.63, R)
>dp4.chr3 2057438 92 - 19779522
---AGAAAGAGAAAAUUUGCAUCGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA----------
---....................(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).---------- ( -26.70, z-score =  -0.18, R)
>droPer1.super_31 71914 92 + 935084
---AGAAAGAUAAAAUUUGCAUCGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA----------
---....................(((((((..((((.......)))).((((((....).))))).....(((((.......)))))))))))).---------- ( -26.70, z-score =  -0.52, R)
>droAna3.scaffold_13266 12988195 77 - 19884421
-----------------------GACUCCGUGGCGCAACGGUAGCGCGUCCGACUCCAGAUCGGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAAGUCU-----
-----------------------((((.....((((.......))))....((((((.((((....))))(((((.......))))).)))))).)))).----- ( -29.50, z-score =  -1.71, R)
>droWil1.scaffold_180700 1819286 95 - 6630534
-----AGUCGAGAAGUCUAACAAGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAACGAU-----
-----.((((.(.(((((....))))).)...((((.......))))...(((((((.((((....))))(((((.......))))).))))))).))))----- ( -30.20, z-score =  -0.90, R)
>droVir3.scaffold_12875 5376997 88 + 20611582
--------AAGAUCAUUUCAUGUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAG---------
--------...........(((((.((((((......)))).)))))))((((((((.((((....))))(((((.......))))).))))))))--------- ( -29.20, z-score =  -1.49, R)
>anoGam1.chrU 56108079 92 - 59568033
UGACGAAUAGGAAAGU---AUGGGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCA----------
.(((...........(---((((....)))))((((.......))))))).((((((.((((....))))(((((.......))))).)))))).---------- ( -28.70, z-score =  -0.51, R)
>consensus
___AGACAGUGAAAUUUUCAAUUGACUCCGUGGCGCAACGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAAA________
.......................(((((((..((((.......)))).((((((....).))))).....(((((.......))))))))))))........... (-26.77 = -26.61 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	16,545,375 – 16,545,472
Length	97
Sequences	11
Columns	105
Reading direction	reverse
Mean pairwise identity	80.94
Shannon entropy	0.42218
G+C content	0.54223
Mean single sequence MFE	-23.95
Consensus MFE	-22.72
Energy contribution	-22.55
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-0.86
Structure conservation index	0.95
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.06
SVM RNA-class probability	0.884213
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16545375 97 - 21146708
-----ACCUCUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAAUUGAAAAUCCCACUGCCU---
-----.....((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))))...................--- ( -23.50, z-score =  -1.18, R)
>droSim1.chr2R 15207185 97 - 19596830
-----ACCUCUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAAUUGAGAAUCCCACUGGCU---
-----..(((((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))))...))).............--- ( -25.30, z-score =  -0.75, R)
>droSec1.super_1 14099502 85 - 14215200
-----AACUCUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAACUGGCU---------------
-----.....((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))).......--------------- ( -23.50, z-score =  -0.75, R)
>droYak2.chr2R 8488821 94 + 21139217
--------UUUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAAUUGAGAAUUGCACCGCCU---
--------.(((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))))..................--- ( -24.30, z-score =  -0.83, R)
>droEre2.scaffold_4845 10693280 102 - 22589142
AUCAACUUUUUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAAUUGAAGAUUCCACUGCCU---
.....(((((((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))))..))))............--- ( -26.10, z-score =  -1.47, R)
>dp4.chr3 2057438 92 + 19779522
----------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCGAUGCAAAUUUUCUCUUUCU---
----------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))....................--- ( -22.70, z-score =  -0.43, R)
>droPer1.super_31 71914 92 - 935084
----------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCGAUGCAAAUUUUAUCUUUCU---
----------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))((((.......)))).....--- ( -23.00, z-score =  -0.75, R)
>droAna3.scaffold_13266 12988195 77 + 19884421
-----AGACUUGACCCCGACGUGAUUUGAACACGCAACCUUCCGAUCUGGAGUCGGACGCGCUACCGUUGCGCCACGGAGUC-----------------------
-----.(((((....((((((((.......))).......(((.....))))))))..((((.......))))....)))))----------------------- ( -22.80, z-score =  -0.67, R)
>droWil1.scaffold_180700 1819286 95 + 6630534
-----AUCGUUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCUUGUUAGACUUCUCGACU-----
-----...(((((.......(((.................((((((.....)))))).((((.......)))))))(((((((....)))))))))))).----- ( -27.30, z-score =  -1.03, R)
>droVir3.scaffold_12875 5376997 88 - 20611582
---------CUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCACAUGAAAUGAUCUU--------
---------.((((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).))))..............-------- ( -23.20, z-score =  -1.06, R)
>anoGam1.chrU 56108079 92 + 59568033
----------UGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCCCAU---ACUUUCCUAUUCGUCA
----------.(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))....---................ ( -21.80, z-score =  -0.51, R)
>consensus
________UCUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUACCGUUGCGCCACGGAGUCAAUUGAAAAUUCCACUGUCU___
...........(((.(((.((((.......))))......((((((.....)))))).((((.......))))..))).)))....................... (-22.72 = -22.55 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:38:52 2011