Locus 3142

Sequence ID	dm3.chr2R
Location	2,834,282 – 2,834,379
Length	97
Max. P	0.998668

overview

Window 8

Location	2,834,282 – 2,834,379
Length	97
Sequences	10
Columns	109
Reading direction	forward
Mean pairwise identity	69.11
Shannon entropy	0.69083
G+C content	0.45602
Mean single sequence MFE	-24.98
Consensus MFE	-22.97
Energy contribution	-21.45
Covariance contribution	-1.52
Combinations/Pair	1.50
Mean z-score	-2.46
Structure conservation index	0.92
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.44
SVM RNA-class probability	0.998668
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2834282 97 + 21146708
AACUAUUUUCUAAAUAUAAAA-----AAGAAAA-------UUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
....(((((((..........-----.))))))-------)........((((((.......))))))....((((((.....)))))).((((........))))... ( -24.50, z-score =  -3.18, R)
>droSim1.chr2R 1651034 109 + 19596830
AACUAACUUCAUAAUAUAAAAUGAAUAGGAAAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
..(((..(((((........))))))))((((.......))))......((((((.......))))))....((((((.....)))))).((((........))))... ( -25.60, z-score =  -2.83, R)
>droSec1.super_1 516330 109 + 14215200
AACUAAUUUCAUAAUAUAAAAUGAAUAAGAAAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
.......(((((........)))))...((((.......))))......((((((.......))))))....((((((.....)))))).((((........))))... ( -24.70, z-score =  -3.09, R)
>droYak2.chr2L 15566878 109 + 22324452
AAUAAUAAAGAAUAAGCUAAUAAGCUAGAAAAAAAAUCGUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
..............((((....)))).((((........))))......((((((.......))))))....((((((.....)))))).((((........))))... ( -26.30, z-score =  -2.37, R)
>dp4.chr3 1124437 108 + 19779522
GAAAAACGUGAAAAUAAGAGGGAAACAAAAACAAAAA-GCUGCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
..................((((...............-((...))....((((((.......)))))).))))(((((.....)))))..((((........))))... ( -26.90, z-score =  -2.08, R)
>droPer1.super_2 1288685 108 + 9036312
GAAAAACGUGAAAAUAAGAGGGAAACAAAAACAAAAA-GCUGGGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
......((((..........(....)...........-..(((((((......)))))))....))))....((((((.....)))))).((((........))))... ( -29.10, z-score =  -2.28, R)
>droWil1.scaffold_180700 5874055 90 + 6630534
-----------------AAAUCAGCAAAAAACAUAAU--UUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
-----------------......((.((((......)--))).))....((((((.......))))))....((((((.....)))))).((((........))))... ( -23.40, z-score =  -2.66, R)
>droMoj3.scaffold_6496 25957777 78 - 26866924
-----------------------------AAAAAAU--GCUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
-----------------------------.......--...........((((((.......))))))....((((((.....)))))).((((........))))... ( -22.50, z-score =  -2.51, R)
>droVir3.scaffold_12476 2639 86 - 9040
-----------------------AAAAACAAAAUAUAACGUUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAC
-----------------------................(((((..((..(((((.......)))))((.(.((((((.....)))))).).))...))..)))))... ( -20.10, z-score =  -2.14, R)
>anoGam1.chr2L 44194329 105 + 48795086
----AACAAGUUGGAAGAAAAUUAUAAAAAGUAGUUGCGACGUGCCUCCUGUGAGAAUCGAACUCACGACCGCUGGUUUACAAGACCAGCGCUCUGCCUACUGAGCUAA
----.....((((((....((((((.....))))))((.....)).))).(((((.......)))))))).(((((((.....)))))))((((........))))... ( -26.70, z-score =  -1.41, R)
>consensus
_A__AAC_UGAAAAUA_AAAA_AAAAAAAAAAAAAUA_GUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAG
.................................................((((((.......))))))....((((((.....)))))).((((........))))... (-22.97 = -21.45 +  -1.52)

alignment

secondary structure

dotplot

Window 9

Location	2,834,282 – 2,834,379
Length	97
Sequences	10
Columns	109
Reading direction	reverse
Mean pairwise identity	69.11
Shannon entropy	0.69083
G+C content	0.45602
Mean single sequence MFE	-26.36
Consensus MFE	-22.75
Energy contribution	-21.61
Covariance contribution	-1.14
Combinations/Pair	1.37
Mean z-score	-0.99
Structure conservation index	0.86
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.36
SVM RNA-class probability	0.989279
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2834282 97 - 21146708
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAA-------UUUUCUU-----UUUUAUAUUUAGAAAAUAGUU
...((((((.(....((.(.(((((.......))))).).))(((((.......))))))))))))..(-------((((((.-----..........))))))).... ( -26.10, z-score =  -1.24, R)
>droSim1.chr2R 1651034 109 - 19596830
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAUUUAUUUUUUCCUAUUCAUUUUAUAUUAUGAAGUUAGUU
((((((((....(((((..((((((((((.......))))))(((((.......)))))..((((.((((.....)))).)))).)))))))))....)).)))))).. ( -28.90, z-score =  -1.59, R)
>droSec1.super_1 516330 109 - 14215200
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAUUUAUUUUUUCUUAUUCAUUUUAUAUUAUGAAAUUAGUU
...((((((.(....((.(.(((((.......))))).).))(((((.......))))))))))))((((.......))))...(((((........)))))....... ( -26.30, z-score =  -1.11, R)
>droYak2.chr2L 15566878 109 - 22324452
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAACGAUUUUUUUUCUAGCUUAUUAGCUUAUUCUUUAUUAUU
...((((((.(....((.(.(((((.......))))).).))(((((.......))))))))))))((((........)))).((((....)))).............. ( -26.00, z-score =  -0.08, R)
>dp4.chr3 1124437 108 - 19779522
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCAGC-UUUUUGUUUUUGUUUCCCUCUUAUUUUCACGUUUUUC
...((((........)))).(((((((((.......))))))(.(((..(((((((......))))((((.-...))))..)))...))).)......)))........ ( -25.90, z-score =  -0.22, R)
>droPer1.super_2 1288685 108 - 9036312
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCCCAGC-UUUUUGUUUUUGUUUCCCUCUUAUUUUCACGUUUUUC
...((((........)))).(((((.......)))))(((..(((((.......)))))((((....))))-...............)))................... ( -25.60, z-score =  -0.23, R)
>droWil1.scaffold_180700 5874055 90 - 6630534
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAA--AUUAUGUUUUUUGCUGAUUU-----------------
.......((((((((((((((((((((((.......))))))(((((.......)))))...........--.))))))..)))))))))).----------------- ( -27.80, z-score =  -1.45, R)
>droMoj3.scaffold_6496 25957777 78 + 26866924
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAGC--AUUUUUU-----------------------------
...(((..(((....((.(.(((((.......))))).).))(((((.......)))))....)))..)))--.......----------------------------- ( -23.30, z-score =  -0.67, R)
>droVir3.scaffold_12476 2639 86 + 9040
GUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAACGUUAUAUUUUGUUUUU-----------------------
(((((....(((.(.(((((.(((((((((.....)))))))))(((.......)))))))).).)))..)))))...........----------------------- ( -26.60, z-score =  -2.41, R)
>anoGam1.chr2L 44194329 105 - 48795086
UUAGCUCAGUAGGCAGAGCGCUGGUCUUGUAAACCAGCGGUCGUGAGUUCGAUUCUCACAGGAGGCACGUCGCAACUACUUUUUAUAAUUUUCUUCCAACUUGUU----
.......(((((((.((.(((((((.......))))))).))(((((.......)))))............))..))))).........................---- ( -27.10, z-score =  -0.91, R)
>consensus
CUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAC_UAUUUUUUUUUAUUU_UUUU_UAUUUUCA_GUU__U_
...((((((......((.(.(((((.......))))).).))(((((.......))))).))))))........................................... (-22.75 = -21.61 +  -1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:31 2011