Locus 15763

Sequence ID dm3.chrX
Location 20,874,899 – 20,875,016
Length 117
Max. P 0.994748
window21722 window21723 window21724

overview

Window 2

Location 20,874,899 – 20,874,989
Length 90
Sequences 12
Columns 106
Reading direction forward
Mean pairwise identity 74.84
Shannon entropy 0.51934
G+C content 0.41255
Mean single sequence MFE -24.00
Consensus MFE -11.80
Energy contribution -11.59
Covariance contribution -0.21
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.920067
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20874899 90 + 22422827
-----------UAGCGACUGAGUCGACGGCCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
-----------...((((...)))).(((((((((....))(((((..(((((....))).((((((((....)))))))-----).))..))))))))))))... ( -28.30, z-score =  -2.45, R)
>droSim1.chrX 16034867 90 + 17042790
-----------CAGCGACUGAGACGACGGCCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
-----------.............(.(((((((((....))(((((..(((((....))).((((((((....)))))))-----).))..))))))))))))).. ( -25.90, z-score =  -1.92, R)
>droSec1.super_8 3157798 90 + 3762037
-----------CAGCGACUGAGACGACGGCCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
-----------.............(.(((((((((....))(((((..(((((....))).((((((((....)))))))-----).))..))))))))))))).. ( -25.90, z-score =  -1.92, R)
>droYak2.chrX 1683929 90 - 21770863
-----------CAGCGACUGAGACGACGGCCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
-----------.............(.(((((((((....))(((((..(((((....))).((((((((....)))))))-----).))..))))))))))))).. ( -25.90, z-score =  -1.92, R)
>droEre2.scaffold_4690 1300588 90 - 18748788
-----------CAGCGACUGAGACGACGGCCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
-----------.............(.(((((((((....))(((((..(((((....))).((((((((....)))))))-----).))..))))))))))))).. ( -25.90, z-score =  -1.92, R)
>droAna3.scaffold_13334 218036 99 - 1562580
--CAGAAAGAGACGAGACUGAGACGUGAAGCAGCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUGGCCGCUU
--.................(((.(((......))))))((((((((..(((((....))).((((((((....)))))))-----).))..))).....))))).. ( -21.60, z-score =  -0.37, R)
>dp4.chrXL_group1e 3036882 85 - 12523060
---CCUUAGUUCCUUAGUUGAGGG------CAUCGUUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUG-------
---((((((........)))))).------((.((((((((.((((((.((((....))))))))))))))))))))...-----..............------- ( -22.70, z-score =  -2.52, R)
>droPer1.super_22 722166 85 + 1688296
---CCUUAGUUCCUUAGUUGAGGG------CAUCGUUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUAUG-------
---((((((........)))))).------((.((((((((.((((((.((((....))))))))))))))))))))...-----..............------- ( -22.70, z-score =  -2.52, R)
>droWil1.scaffold_180702 2409210 102 + 4511350
----CAGAGAACCCACACUGAGGGAACACCAGGCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUUUGAUUGAAGUGAUUAUAUGGCCGCUG
----.......(((.......))).......((((((....(((((..(((((..((..(...((((((....)))))))..)))))))..)))))..)).)))). ( -25.10, z-score =  -1.21, R)
>droMoj3.scaffold_6473 4747877 90 + 16943266
-----AUAGUAACUGGCUCGAAGG-----CUC-GGAUUGCCGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUUGGACCACUU
-----........(((..(((.((-----(..-.....))).((((..(((((....))).((((((((....)))))))-----).))..)))))))..)))... ( -22.10, z-score =  -1.72, R)
>droVir3.scaffold_12970 5186078 81 + 11907090
--------------GGCUCGAAGA-----UUU-GGAUUGGCGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUUGGACCACUU
--------------((..(((...-----...-......(((((((((.((((....))))))))))))).....(((((-----.....))))))))..)).... ( -18.80, z-score =  -1.75, R)
>droGri2.scaffold_15081 4104858 96 - 4274704
CAACUACAAUAAGGAGCCCGAAGG-----UUUCGGAUUCACGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU-----GAAGUGAUUAUUGGGGCACUU
....((((((..((((((....))-----))))..)))...)))..(((((((((((((..((((((((....)))))))-----)...)))))).)))))))... ( -23.10, z-score =  -1.83, R)
>consensus
___________CAGCGACUGAGGCGAC__CCAUCGCUUGCGGUAAUUGCUUCAUAAUUGAACAAUUAUGCAAACGUGAUU_____GAAGUGAUUAUAUGGCCGCUU
.................................((....))(((((..((((((((((....))))))((....)).........))))..))))).......... (-11.80 = -11.59 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,874,899 – 20,874,989
Length 90
Sequences 12
Columns 106
Reading direction reverse
Mean pairwise identity 74.84
Shannon entropy 0.51934
G+C content 0.41255
Mean single sequence MFE -21.84
Consensus MFE -11.16
Energy contribution -11.57
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -2.57
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.73
SVM RNA-class probability 0.994748
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20874899 90 - 22422827
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCGUCGACUCAGUCGCUA-----------
..((((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))))((((...))))...----------- ( -28.09, z-score =  -3.70, R)
>droSim1.chrX 16034867 90 - 17042790
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCGUCGUCUCAGUCGCUG-----------
.(((((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))(.(......).)))).----------- ( -26.39, z-score =  -3.17, R)
>droSec1.super_8 3157798 90 - 3762037
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCGUCGUCUCAGUCGCUG-----------
.(((((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))(.(......).)))).----------- ( -26.39, z-score =  -3.17, R)
>droYak2.chrX 1683929 90 + 21770863
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCGUCGUCUCAGUCGCUG-----------
.(((((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))(.(......).)))).----------- ( -26.39, z-score =  -3.17, R)
>droEre2.scaffold_4690 1300588 90 + 18748788
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCGUCGUCUCAGUCGCUG-----------
.(((((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))(.(......).)))).----------- ( -26.39, z-score =  -3.17, R)
>droAna3.scaffold_13334 218036 99 + 1562580
AAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGCUGCUUCACGUCUCAGUCUCGUCUCUUUCUG--
(((((((..............-----......((((((.((((((((((....)).))))))))..))))))))))))).........................-- ( -19.05, z-score =  -1.70, R)
>dp4.chrXL_group1e 3036882 85 + 12523060
-------CAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAACGAUG------CCCUCAACUAAGGAACUAAGG---
-------..............-----.....(((((((.((((((((((....)).))))))))..)))))))...------.(((......)))........--- ( -17.40, z-score =  -3.08, R)
>droPer1.super_22 722166 85 - 1688296
-------CAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAACGAUG------CCCUCAACUAAGGAACUAAGG---
-------..............-----.....(((((((.((((((((((....)).))))))))..)))))))...------.(((......)))........--- ( -17.40, z-score =  -3.08, R)
>droWil1.scaffold_180702 2409210 102 - 4511350
CAGCGGCCAUAUAAUCACUUCAAUCAAAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGCCUGGUGUUCCCUCAGUGUGGGUUCUCUG----
(((.((((.......((((........(((((((((((.((((((((((....)).))))))))..)))))))..))))........))))..)).)).)))---- ( -23.59, z-score =  -1.26, R)
>droMoj3.scaffold_6473 4747877 90 - 16943266
AAGUGGUCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGGCAAUCC-GAG-----CCUUCGAGCCAGUUACUAU-----
((.(((..(............-----......((((.(((((((....)))))))))))......(((.....-..)-----))...)..))).)).....----- ( -17.70, z-score =  -1.52, R)
>droVir3.scaffold_12970 5186078 81 - 11907090
AAGUGGUCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGCCAAUCC-AAA-----UCUUCGAGCC--------------
(((((((......))))))).-----......(((.((.((((((((((....)).)))))))).)).)))..-...-----..........-------------- ( -12.80, z-score =  -1.51, R)
>droGri2.scaffold_15081 4104858 96 + 4274704
AAGUGCCCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGUGAAUCCGAAA-----CCUUCGGGCUCCUUAUUGUAGUUG
....((..((((((.......-----..((((((((((((((((....))))))...))))..)))))).(((((..-----...)))))....))))))..)).. ( -20.50, z-score =  -2.28, R)
>consensus
AAGCGGCCAUAUAAUCACUUC_____AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGG__GUCGCCUCAGUCGCGG___________
................................((((((.((((((((((....)).))))))))..)))))).................................. (-11.16 = -11.57 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,874,914 – 20,875,016
Length 102
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 78.24
Shannon entropy 0.43555
G+C content 0.41830
Mean single sequence MFE -23.79
Consensus MFE -11.16
Energy contribution -11.57
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -2.02
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763520
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20874914 102 - 22422827
-------------GGGAAACGCACAUAAACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
-------------.(....)((.(((.......(((((....)).))).............-----.....(((((((.((((((((((....)).))))))))..)))))))))))).. ( -27.00, z-score =  -2.25, R)
>droSim1.chrX 16034882 102 - 17042790
-------------GGGAAACGCACAUAUACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
-------------.(....)((.(((.......(((((....)).))).............-----.....(((((((.((((((((((....)).))))))))..)))))))))))).. ( -27.00, z-score =  -2.17, R)
>droSec1.super_8 3157813 102 - 3762037
-------------GGGAAACGCACAUAUACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
-------------.(....)((.(((.......(((((....)).))).............-----.....(((((((.((((((((((....)).))))))))..)))))))))))).. ( -27.00, z-score =  -2.17, R)
>droYak2.chrX 1683944 102 + 21770863
-------------GGAAAACACACAUAAACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
-------------.....................((......))((((((...........-----.....(((((((.((((((((((....)).))))))))..))))))))))))). ( -25.39, z-score =  -2.64, R)
>droEre2.scaffold_4690 1300603 102 + 18748788
-------------GGAAAACACACAUAAACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
-------------.....................((......))((((((...........-----.....(((((((.((((((((((....)).))))))))..))))))))))))). ( -25.39, z-score =  -2.64, R)
>droAna3.scaffold_13334 218060 115 + 1562580
GGGAACUGGGAACUCGGAAAGCACAUAAACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGCUGCUUC
.....((((....)))).(((((..........(((((....)).))).............-----.....(((((((.((((((((((....)).))))))))..))))))).))))). ( -27.60, z-score =  -1.13, R)
>dp4.chrXL_group1e 3036900 86 + 12523060
--------------------------ACACAGAGAAACA--GGGGGGCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAACGAUGCCC-
--------------------------.............--...((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))- ( -21.49, z-score =  -2.92, R)
>droPer1.super_22 722184 84 - 1688296
--------------------------ACACACAGAAACA--G--GGGCAUAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAACGAUGCCC-
--------------------------.............--.--((((((...........-----.....(((((((.((((((((((....)).))))))))..)))))))))))))- ( -21.49, z-score =  -3.91, R)
>droWil1.scaffold_180702 2409232 106 - 4511350
--------------GGGAAAAACAGUAAACGGAGAAACAUCAGCGGCCAUAUAAUCACUUCAAUCAAAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGCCUGGUG
--------------.......................((((((.((........))...............(((((((.((((((((((....)).))))))))..))))))).)))))) ( -18.90, z-score =  -0.00, R)
>droMoj3.scaffold_6473 4747893 101 - 16943266
-------------GUGACGAGGACAUAAACAUUGGCGCCUAAGUGGUCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGGCAAUCCGAGCCU-
-------------((((.((((........(((((.(((.....)))))))).....))))-----..))))((((.(((((((....)))))))))))......(((.......))).- ( -24.12, z-score =  -1.43, R)
>droVir3.scaffold_12970 5186085 101 - 11907090
-------------GUGACGAGGGCAUAAACAUUGUCGCCUAAGUGGUCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGCCAAUCCAAAUCU-
-------------((((...(((((((.....))).))))(((((((......))))))).-----..))))(((.((.((((((((((....)).)))))))).)).)))........- ( -21.80, z-score =  -1.81, R)
>droGri2.scaffold_15081 4104879 102 + 4274704
-------------GUGAAGAGGACAUAAACACUGCCGCCUAAGUGCCCCAAUAAUCACUUC-----AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACGUGAAUCCGAAACCU
-------------.(((((.((.......((((........)))).........)).))))-----).((((((((((((((((....))))))...))))..))))))........... ( -18.29, z-score =  -1.10, R)
>consensus
_____________GGGAAAAGCACAUAAACAGAGGCGCAUAAGCGGCCAUAUAAUCACUUC_____AAUCACGUUUGCAUAAUUGUUCAAUUAUGAAGCAAUUACCGCAAGCGAUGGCCG
........................................................................((((((.((((((((((....)).))))))))..))))))........ (-11.16 = -11.57 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:05:27 2011