Locus 3962

Sequence ID dm3.chr2R
Location 9,319,278 – 9,319,379
Length 101
Max. P 0.988250
window5423 window5424

overview

Window 3

Location 9,319,278 – 9,319,379
Length 101
Sequences 12
Columns 112
Reading direction forward
Mean pairwise identity 77.35
Shannon entropy 0.48122
G+C content 0.51434
Mean single sequence MFE -30.04
Consensus MFE -26.81
Energy contribution -25.81
Covariance contribution -1.00
Combinations/Pair 1.41
Mean z-score -1.11
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.54
SVM RNA-class probability 0.948295
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9319278 101 + 21146708
UAUGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGAUAUUUUUUAUUUCUGAACAUCC----
..((((((((..((((.........))))((((.(((.....-------((((.....))))))).))))......))))))))........................---- ( -29.20, z-score =  -1.05, R)
>droGri2.scaffold_15245 203951 92 + 18325388
CAUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGCCGCGGGUUCGAUCCCCCCAUGGGCCAGGAUUGUCUUCUUUU-------------
..((((((((.......((.((((...((((..(....)..)-------)))...))))))(((......)))...))))))))(((......)))...------------- ( -30.90, z-score =  -0.51, R)
>droMoj3.scaffold_6496 25288206 90 + 26866924
UGUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCCCAUGGGCCAAGAGU-UCUUAGUU--------------
..((((((((((((.(.(((......)))...).))))))..-------.(((.....)))(((......))).....)))))).....-........-------------- ( -29.50, z-score =  -0.70, R)
>droVir3.scaffold_12875 15829587 96 - 20611582
CGGGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGCCGCGGGUUCGAUCCCCCCAUGGGCCAAUUUAUAUUUUUCAAUUUU---------
...(((((((.......((.((((...((((..(....)..)-------)))...))))))(((......)))...)))))))....................--------- ( -29.80, z-score =  -0.35, R)
>droPer1.super_2 8066107 92 + 9036312
UGUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGAAACUACUUUUUUC-------------
(.((((((((((((.(.(((......)))...).))))))..-------.(((.....)))(((......))).....)))))).).............------------- ( -29.70, z-score =  -1.03, R)
>dp4.chr3 6225561 92 - 19779522
UGUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGAAAAUACUUUUUUC-------------
..((((((((((((.(.(((......)))...).))))))..-------.(((.....)))(((......))).....))))))(((((.....)))))------------- ( -30.30, z-score =  -1.41, R)
>droEre2.scaffold_4845 6091128 95 - 22589142
CAUGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGGAAACCUUUUUUUUUAA----------
..((((((((..((((.........))))((((.(((.....-------((((.....))))))).))))......))))))))(....)............---------- ( -30.00, z-score =  -1.23, R)
>droYak2.chr2R 13499346 97 - 21139217
CAUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGGAUUCUUUUUUAUUUUGAU--------
..((((((((((((.(.(((......)))...).))))))..-------.(((.....)))(((......))).....))))))....................-------- ( -29.60, z-score =  -0.69, R)
>droSec1.super_1 6837595 96 + 14215200
CAUGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGACAAUUUUUAUUUUUGAA---------
..((((((((..((((.........))))((((.(((.....-------((((.....))))))).))))......))))))))...................--------- ( -29.20, z-score =  -1.27, R)
>anoGam1.chr2R 13947286 102 - 62725911
---GGCUCCAUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGUGAGUUCGAUCCUCUCUGGAGCCAUAGAGAAUGUUUUUAUAUUCCAAGCUAG
---(((((((((((...))))...((((.((((.(((....(-------(((....).))).))).)))).)))).))))))).(((.((((((....))))))....))). ( -34.30, z-score =  -2.33, R)
>droAna3.scaffold_13266 10206574 92 - 19884421
---GGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAA-------CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAUA---AAUAUUUUGCUAUUAC-------
---(((((((..((((.........))))((((.(((.....-------((((.....))))))).))))......)))))))...---................------- ( -28.20, z-score =  -1.20, R)
>triCas2.chrUn_43 98015 94 - 275627
GUCGGUUCGUUAGCUCAGGUGGUUAGAGCACCGCACUAAGCAGCAGCCUUGCGGAGGUCGUAGGUUCGAAUCCUACAUGAGCCAAACUUUUUUU------------------
...((((((((.(((.(((((((......))))).)).)))))).(((((...))))).(((((.......)))))..)))))...........------------------ ( -29.80, z-score =  -1.57, R)
>consensus
CAUGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAA_______CGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGAAAUUUUUUUUUUCU____________
...(((((((..((((.........))))((((.(((............((((.....))))))).))))......)))))))............................. (-26.81 = -25.81 +  -1.00)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 9,319,278 – 9,319,379
Length 101
Sequences 12
Columns 112
Reading direction reverse
Mean pairwise identity 77.35
Shannon entropy 0.48122
G+C content 0.51434
Mean single sequence MFE -28.72
Consensus MFE -25.53
Energy contribution -24.99
Covariance contribution -0.54
Combinations/Pair 1.29
Mean z-score -1.68
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988250
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9319278 101 - 21146708
----GGAUGUUCAGAAAUAAAAAAUAUCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCAUA
----(((((((...........)))))))(((((((..(((.......)))(((.....))).-------.............((((.........))))..)))))))... ( -30.70, z-score =  -2.25, R)
>droGri2.scaffold_15245 203951 92 - 18325388
-------------AAAAGAAGACAAUCCUGGCCCAUGGGGGGAUCGAACCCGCGGCCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCAUG
-------------...............(((((((((.(((.......))).).....(((.(-------(.....)).))).((((.........))))..)))))))).. ( -28.70, z-score =  -0.44, R)
>droMoj3.scaffold_6496 25288206 90 - 26866924
--------------AACUAAGA-ACUCUUGGCCCAUGGGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCACA
--------------........-.....((((((((.(((((.(((......))))))))((.-------......)).....((((.........))))..)))))))).. ( -29.20, z-score =  -1.55, R)
>droVir3.scaffold_12875 15829587 96 + 20611582
---------AAAAUUGAAAAAUAUAAAUUGGCCCAUGGGGGGAUCGAACCCGCGGCCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCCCG
---------....................((((((((.(((.......))).).....(((.(-------(.....)).))).((((.........))))..)))))))... ( -27.20, z-score =  -0.05, R)
>droPer1.super_2 8066107 92 - 9036312
-------------GAAAAAAGUAGUUUCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCACA
-------------...............((((((((..(((.......)))(((.....))).-------....((((.((..(((......))))).)))))))))))).. ( -28.70, z-score =  -1.39, R)
>dp4.chr3 6225561 92 + 19779522
-------------GAAAAAAGUAUUUUCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCACA
-------------(((((.....)))))((((((((..(((.......)))(((.....))).-------....((((.((..(((......))))).)))))))))))).. ( -29.70, z-score =  -2.09, R)
>droEre2.scaffold_4845 6091128 95 + 22589142
----------UUAAAAAAAAAGGUUUCCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCAUG
----------..................((((((((..(((.......)))(((.....))).-------.............((((.........))))..)))))))).. ( -28.60, z-score =  -1.93, R)
>droYak2.chr2R 13499346 97 + 21139217
--------AUCAAAAUAAAAAAGAAUCCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCAUG
--------....................((((((((..(((.......)))(((.....))).-------....((((.((..(((......))))).)))))))))))).. ( -28.80, z-score =  -2.09, R)
>droSec1.super_1 6837595 96 - 14215200
---------UUCAAAAAUAAAAAUUGUCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCAUG
---------...................((((((((..(((.......)))(((.....))).-------.............((((.........))))..)))))))).. ( -28.60, z-score =  -2.44, R)
>anoGam1.chr2R 13947286 102 + 62725911
CUAGCUUGGAAUAUAAAAACAUUCUCUAUGGCUCCAGAGAGGAUCGAACUCACGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAGCUGAGCUAUGGAGCC---
.......................(((((((((((.((.((((.(((......))).))))(((-------((........))))).........)))))))))))))..--- ( -29.20, z-score =  -2.03, R)
>droAna3.scaffold_13266 10206574 92 + 19884421
-------GUAAUAGCAAAAUAUU---UAUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG-------UUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCC---
-------................---...(((((((..(((.......)))(((.....))).-------.............((((.........))))..)))))))--- ( -26.30, z-score =  -1.54, R)
>triCas2.chrUn_43 98015 94 + 275627
------------------AAAAAAAGUUUGGCUCAUGUAGGAUUCGAACCUACGACCUCCGCAAGGCUGCUGCUUAGUGCGGUGCUCUAACCACCUGAGCUAACGAACCGAC
------------------.......(((.((((((.(((((.......)))))((.(.(((((.(((....)))...))))).).))........)))))))))........ ( -28.90, z-score =  -2.37, R)
>consensus
____________AAAAAAAAAAAAUUUCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCG_______UUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCAUG
.............................(((((((..(((.......)))(((.....))).....................((((.........))))..)))))))... (-25.53 = -24.99 +  -0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:20:03 2011