Locus 3833

Sequence ID dm3.chr2R
Location 8,223,920 – 8,224,000
Length 80
Max. P 0.997135
window5254 window5255

overview

Window 4

Location 8,223,920 – 8,224,000
Length 80
Sequences 14
Columns 106
Reading direction forward
Mean pairwise identity 91.30
Shannon entropy 0.17533
G+C content 0.56844
Mean single sequence MFE -30.56
Consensus MFE -28.12
Energy contribution -28.35
Covariance contribution 0.23
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959749
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8223920 80 + 21146708
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>droSim1.chr2R 6692663 80 + 19596830
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>droSec1.super_1 5769853 80 + 14215200
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>droYak2.chr2R 12412764 80 - 21139217
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>droEre2.scaffold_4845 5020693 80 - 22589142
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>droAna3.scaffold_13266 5515682 80 + 19884421
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -2.03, R)
>dp4.chr3 16981574 80 - 19779522
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>droPer1.super_2 6048362 80 - 9036312
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>droWil1.scaffold_180745 463085 80 + 2843958
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>droVir3.scaffold_12875 13998727 80 - 20611582
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>droMoj3.scaffold_6496 23396889 80 + 26866924
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>droGri2.scaffold_15112 3672713 80 - 5172618
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-----------------------
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......----------------------- ( -30.00, z-score =  -1.74, R)
>anoGam1.chr2L 19560199 103 - 48795086
UAGCCGUGAUCGUC---UAGUGGUUAGGACCCUACGUUGUGGCCGUAGUAACCCAGGUUCGAAUCCUGGUCACGGCAGUGUUGCCAGCAGUCGAAAGUCUACUGGG
..(((((((....(---((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).......((((.((.(....).)).)))). ( -40.60, z-score =  -2.82, R)
>triCas2.ChLG7 15875478 69 - 17478683
UCGCCGUGAUCGUCGGCUAGUGGUUAGGA-----------GGCCGUAGUAAACCAGGUUCGAAUCCUGGUCACGGCUAGG--------------------------
..(((((((......((((.(((((....-----------)))))))))...(((((.......))))))))))))....-------------------------- ( -27.20, z-score =  -2.33, R)
>consensus
UAGCCGUGAUCGUC___UAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG_______________________
..(((((((............(((((.(((.....))).)))))........(((((.......)))))))))))).............................. (-28.12 = -28.35 +   0.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,223,920 – 8,224,000
Length 80
Sequences 14
Columns 106
Reading direction reverse
Mean pairwise identity 91.30
Shannon entropy 0.17533
G+C content 0.56844
Mean single sequence MFE -31.77
Consensus MFE -28.92
Energy contribution -29.36
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -3.23
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.04
SVM RNA-class probability 0.997135
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8223920 80 - 21146708
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>droSim1.chr2R 6692663 80 - 19596830
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>droSec1.super_1 5769853 80 - 14215200
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>droYak2.chr2R 12412764 80 + 21139217
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>droEre2.scaffold_4845 5020693 80 + 22589142
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>droAna3.scaffold_13266 5515682 80 - 19884421
-----------------------CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.34, R)
>dp4.chr3 16981574 80 + 19779522
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>droPer1.super_2 6048362 80 + 9036312
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>droWil1.scaffold_180745 463085 80 - 2843958
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>droVir3.scaffold_12875 13998727 80 + 20611582
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>droMoj3.scaffold_6496 23396889 80 - 26866924
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>droGri2.scaffold_15112 3672713 80 + 5172618
-----------------------CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA---GACGAUCACGGCUA
-----------------------.......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -31.70, z-score =  -3.00, R)
>anoGam1.chr2L 19560199 103 + 48795086
CCCAGUAGACUUUCGACUGCUGGCAACACUGCCGUGACCAGGAUUCGAACCUGGGUUACUACGGCCACAACGUAGGGUCCUAACCACUA---GACGAUCACGGCUA
.(((((((........))))))).......((((((((((((.......)))))(((.(((((.......)))))(((....)))....---)))..))))))).. ( -39.00, z-score =  -3.47, R)
>triCas2.ChLG7 15875478 69 + 17478683
--------------------------CCUAGCCGUGACCAGGAUUCGAACCUGGUUUACUACGGCC-----------UCCUAACCACUAGCCGACGAUCACGGCGA
--------------------------....((((((((((((.......))))).......((((.-----------............))))....))))))).. ( -25.42, z-score =  -3.76, R)
>consensus
_______________________CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUA___GACGAUCACGGCUA
..............................((((((((((((.......)))))(((.(((((.......)))))(((....))).......)))..))))))).. (-28.92 = -29.36 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:17:39 2011