Locus 1882

Sequence ID dm3.chr2L
Location 14,530,526 – 14,530,617
Length 91
Max. P 0.994108
window2596 window2597

overview

Window 6

Location 14,530,526 – 14,530,617
Length 91
Sequences 14
Columns 105
Reading direction forward
Mean pairwise identity 79.06
Shannon entropy 0.47174
G+C content 0.55919
Mean single sequence MFE -32.15
Consensus MFE -29.71
Energy contribution -29.32
Covariance contribution -0.38
Combinations/Pair 1.40
Mean z-score -2.03
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.67
SVM RNA-class probability 0.994108
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14530526 91 + 23011544
--------AAAUAUCAAAAA-GCUAUUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
--------............-........((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -1.85, R)
>droWil1.scaffold_181096 4526278 91 + 12416693
---------UGAAAAAAAAAACCUCAUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCUUGGCGGGCGAGCAUUCU-ACCUCUGAACCACCGAUGCU----
---------....................((((((((((((.......)))))(((((((((...))))))).)).....-............))))))).---- ( -38.30, z-score =  -3.95, R)
>droVir3.scaffold_12963 205121 91 - 20206255
------AGCUGACGAAAAAAUAAAUU---GCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
------....................---((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -1.72, R)
>droMoj3.scaffold_6500 23190625 94 + 32352404
------AAAUAUAAAAAAAAAAGAUUUCUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
------.......................((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -2.28, R)
>droGri2.scaffold_15252 5723939 100 - 17193109
AAGUAUGCUAGAUCAAAAAAGUUAUUCUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
.............................((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -0.96, R)
>droPer1.super_1 8485218 77 + 10282868
------------------------AUCUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUGACCACUAUACUAUCGAGGAU----
------------------------.....(((.(((.((((.......))))((((((((((.......)))))).....)))).........))).))).---- ( -28.20, z-score =  -1.19, R)
>dp4.chr4_group1 4155954 96 - 5278887
--------AUAUCCAAAAAAAGUACUGCUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCUUAUU
--------.....................((((((((((((.......)))))((((((.((...)).)))).)).....-............)))))))..... ( -32.20, z-score =  -1.49, R)
>droAna3.scaffold_12943 3040220 92 + 5039921
--------AUGAUCAAAAAAUAAUUUCCUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
--------.....................((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -1.84, R)
>droEre2.scaffold_4929 6286843 90 + 26641161
--------AAGAUCAAAAAGGAUAUU--UGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
--------...(((......)))...--.((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.30, z-score =  -1.55, R)
>droYak2.chr2L 14640779 90 + 22324452
--------AAAAUCAAAAUAUGUAUU--UGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
--------..................--.((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -1.88, R)
>droSec1.super_3 794187 90 + 7220098
---------AUUAUCAAAAA-AGCUAUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
---------...........-........((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -1.84, R)
>droSim1.chr2L 14279161 90 + 22036055
---------AUUAUCAAAAA-AUCUAUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
---------...........-........((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -2.12, R)
>anoGam1.chr2L 14910695 92 + 48795086
--------AACUAUAAAAAACACUCGUCUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU-ACCACUGAACCACCGAUGCU----
--------.....................((((((((((((.......)))))((((((.((...)).)))).)).....-............))))))).---- ( -32.20, z-score =  -2.04, R)
>apiMel3.Group14 6137489 90 - 8318479
----------GAAUGAAAAAAAUAAACUUGCACUGCCCGGGAAUCGAACCCGGGUCGCAAGAAUGGGAAUCUUGCAUGAU-ACCACUACACCAGCAGUGCU----
----------...................((((((((((((.......)))))...((((((.......)))))).....-............))))))).---- ( -29.30, z-score =  -3.73, R)
>consensus
________AAGAACAAAAAA_AUAUUUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCU_ACCACUGAACCACCGAUGCU____
.............................((((((((((((.......)))))((((((.((...)).)))).))..................)))))))..... (-29.71 = -29.32 +  -0.38)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 7

Location 14,530,526 – 14,530,617
Length 91
Sequences 14
Columns 105
Reading direction reverse
Mean pairwise identity 79.06
Shannon entropy 0.47174
G+C content 0.55919
Mean single sequence MFE -35.54
Consensus MFE -33.74
Energy contribution -33.11
Covariance contribution -0.62
Combinations/Pair 1.52
Mean z-score -1.70
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988161
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14530526 91 - 23011544
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAAUAGC-UUUUUGAUAUUU--------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))........-............-------- ( -35.90, z-score =  -1.51, R)
>droWil1.scaffold_181096 4526278 91 - 12416693
----AGCAUCGGUGGUUCAGAGGU-AGAAUGCUCGCCCGCCAAGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAUGAGGUUUUUUUUUUCA---------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))...(((((.......)))))--------- ( -38.70, z-score =  -2.23, R)
>droVir3.scaffold_12963 205121 91 + 20206255
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGC---AAUUUAUUUUUUCGUCAGCU------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))---....................------ ( -35.90, z-score =  -1.43, R)
>droMoj3.scaffold_6500 23190625 94 - 32352404
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAGAAAUCUUUUUUUUUUAUAUUU------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).......................------ ( -35.90, z-score =  -1.97, R)
>droGri2.scaffold_15252 5723939 100 + 17193109
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAGAAUAACUUUUUUGAUCUAGCAUACUU
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))............................. ( -35.90, z-score =  -1.05, R)
>droPer1.super_1 8485218 77 - 10282868
----AUCCUCGAUAGUAUAGUGGUCAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAGAU------------------------
----.((((((((........((((......(((((.......))))).))))((((.......)))))))))))).....------------------------ ( -31.80, z-score =  -1.83, R)
>dp4.chr4_group1 4155954 96 + 5278887
AAUAAGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAGCAGUACUUUUUUUGGAUAU--------
.....(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).....................-------- ( -35.90, z-score =  -1.03, R)
>droAna3.scaffold_12943 3040220 92 - 5039921
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAGGAAAUUAUUUUUUGAUCAU--------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).....................-------- ( -35.90, z-score =  -1.29, R)
>droEre2.scaffold_4929 6286843 90 - 26641161
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCA--AAUAUCCUUUUUGAUCUU--------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).--..................-------- ( -35.90, z-score =  -1.52, R)
>droYak2.chr2L 14640779 90 - 22324452
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCA--AAUACAUAUUUUGAUUUU--------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).--..................-------- ( -35.90, z-score =  -1.85, R)
>droSec1.super_3 794187 90 - 7220098
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAUAGCU-UUUUUGAUAAU---------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))........-...........--------- ( -35.90, z-score =  -1.52, R)
>droSim1.chr2L 14279161 90 - 22036055
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAUAGAU-UUUUUGAUAAU---------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......))))))))))))........-...........--------- ( -35.90, z-score =  -1.74, R)
>anoGam1.chr2L 14910695 92 - 48795086
----AGCAUCGGUGGUUCAGUGGU-AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAGACGAGUGUUUUUUAUAGUU--------
----.(((((((..((((......-.))))((.(((((((...)))))))))(((((.......)))))))))))).....................-------- ( -35.90, z-score =  -1.22, R)
>apiMel3.Group14 6137489 90 + 8318479
----AGCACUGCUGGUGUAGUGGU-AUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCAGUGCAAGUUUAUUUUUUUCAUUC----------
----.((((((((((((......)-))))(((((((.......)))))))..(((((.......))))))))))))...................---------- ( -32.20, z-score =  -3.68, R)
>consensus
____AGCAUCGGUGGUUCAGUGGU_AGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAAAUAU_UUUUUUAUUCUU________
.....(((((((..((((........))))((.(((((((...)))))))))(((((.......))))))))))))............................. (-33.74 = -33.11 +  -0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:43 2011