Locus 923

Sequence ID dm3.chr2L
Location 6,799,737 – 6,799,817
Length 80
Max. P 0.998274
window1250 window1251

overview

Window 0

Location 6,799,737 – 6,799,817
Length 80
Sequences 13
Columns 95
Reading direction forward
Mean pairwise identity 71.06
Shannon entropy 0.61627
G+C content 0.56129
Mean single sequence MFE -30.12
Consensus MFE -28.15
Energy contribution -24.99
Covariance contribution -3.16
Combinations/Pair 2.43
Mean z-score -1.20
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984489
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6799737 80 + 23011544
--------CCACAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -0.77, R)
>anoGam1.chr3L 36924764 88 - 41284009
CCUCAUAGCAAAGGGGUCCUGUGGCGCAAUGGAU-AACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGG------
(((........)))(((((((((((((.......-...))))).......(((((....)))))((((.......))))))))))))..------ ( -27.90, z-score =  -0.55, R)
>droGri2.scaffold_14906 200108 82 - 14172833
--------CCAACUGCCCGGCUAGCUCAGUCGGU-AGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAA----
--------.....((((((((..((((.......-.))))....((((((.......))))))(((((.......)))))))))))))...---- ( -32.80, z-score =  -1.91, R)
>droMoj3.scaffold_6540 19666616 79 - 34148556
-------------UGGCGCCGUGGCUUAGUUGGUUAAAGCGCCUGUCUAGUAAACAGGAGAUCGUGAGUUCGAAUCUCGCCGGGGCCUUUGC---
-------------.((.(((.((((((((..(((......)))...)))).......(((((((......)).))))))))).)))))....--- ( -24.70, z-score =  -0.04, R)
>droVir3.scaffold_12875 10427360 75 + 20611582
-------------CGCCUCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGAGGAUUGUGGGUUCGAGUCCCAUCUGAGGUAA------
-------------.(((((((..((((.......-.)))).(((((.......))))).....(((((.......))))))))))))..------ ( -28.80, z-score =  -1.74, R)
>droWil1.scaffold_180708 7702623 80 + 12563649
-------CCUGAAAGCUCCAGUGGCCUAAUGGA--AAGGCAUCGGCCUCCUAAGCCGAGGAUUGUGGGUUCGAGUCCCACCUGGAGUAA------
-------.......(((((((..((((......--.)))).(((((.......))))).....(((((.......))))))))))))..------ ( -30.50, z-score =  -1.85, R)
>droPer1.super_5 4707410 78 + 6813705
--------UAACAAGCCCCAGUGGCCUAAUGGAG-AAGGCACCGGCCUCCUAAGCCGGGGAUUGUGGGUUCAAGUCCCACCUGGGGU--------
--------......(((((((..((((.......-.)))).(((((.......))))).....(((((.......))))))))))))-------- ( -34.30, z-score =  -1.39, R)
>dp4.chr3 13014949 80 + 19779522
--------CGAUAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -1.06, R)
>droAna3.scaffold_12928 260993 83 + 771024
-----------UAGGACCCCAUGGUUCAAUGAUU-AAGAUAUCUGCCUGUAAAUCGUAAGAUCGUCGGUUCGAUUCCCAGCAGAAAAAUCUUUAU
-----------..(((((....))))).......-(((((.(((((.((..(((((...(.....)....)))))..)))))))...)))))... ( -20.00, z-score =  -2.08, R)
>droEre2.scaffold_4929 15715912 80 + 26641161
--------CGACAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -0.95, R)
>droYak2.chr2L 16215580 80 - 22324452
--------CAACAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -1.10, R)
>droSec1.super_3 2338511 80 + 7220098
--------CAACAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -1.10, R)
>droSim1.chr2L 6601146 80 + 22036055
--------CAACAUGCCCCAGUGGCCUAAUGGAU-AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA------
--------.....((((((((..((((.......-.))))..((((.......))))((((((.((....))))))))..)))))))).------ ( -32.10, z-score =  -1.10, R)
>consensus
________CAACAUGCCCCAGUGGCCUAAUGGAU_AAGGCAUCGGCCUCCUAAGCCGGGGAUUGUGGGUUCGAGUCCCAUCUGGGGUAA______
..............(((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))........ (-28.15 = -24.99 +  -3.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,799,737 – 6,799,817
Length 80
Sequences 13
Columns 95
Reading direction reverse
Mean pairwise identity 71.06
Shannon entropy 0.61627
G+C content 0.56129
Mean single sequence MFE -28.85
Consensus MFE -23.46
Energy contribution -21.27
Covariance contribution -2.19
Combinations/Pair 2.21
Mean z-score -1.97
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.31
SVM RNA-class probability 0.998274
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6799737 80 - 23011544
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUGUGG--------
------....(((....)))........(((((..((((((((((((((((....)))))-.....)))))))...))))..)))))-------- ( -30.00, z-score =  -1.35, R)
>anoGam1.chr3L 36924764 88 + 41284009
------CCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUU-AUCCAUUGCGCCACAGGACCCCUUUGCUAUGAGG
------....((((((((((.......))))).....((((((.....)))))).((((.-.......))))..)))))..((((......)))) ( -25.60, z-score =  -1.13, R)
>droGri2.scaffold_14906 200108 82 + 14172833
----UUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCU-ACCGACUGAGCUAGCCGGGCAGUUGG--------
----......((((((((((.......)))))(.(((((((((.....)))))).((((.-.......)))).....)))).)))))-------- ( -31.70, z-score =  -2.54, R)
>droMoj3.scaffold_6540 19666616 79 + 34148556
---GCAAAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCA-------------
---.....(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).))).------------- ( -25.20, z-score =  -2.53, R)
>droVir3.scaffold_12875 10427360 75 - 20611582
------UUACCUCAGAUGGGACUCGAACCCACAAUCCUCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGAGGCG-------------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).))))))..------------- ( -27.70, z-score =  -2.79, R)
>droWil1.scaffold_180708 7702623 80 - 12563649
------UUACUCCAGGUGGGACUCGAACCCACAAUCCUCGGCUUAGGAGGCCGAUGCCUU--UCCAUUAGGCCACUGGAGCUUUCAGG-------
------...(((((((((((.......))))).......((((((((((((....)))))--....))))))).))))))........------- ( -31.90, z-score =  -2.74, R)
>droPer1.super_5 4707410 78 - 6813705
--------ACCCCAGGUGGGACUUGAACCCACAAUCCCCGGCUUAGGAGGCCGGUGCCUU-CUCCAUUAGGCCACUGGGGCUUGUUA--------
--------.(((((((((((.......))))).......((((((((((((....)))))-)).....))))).)))))).......-------- ( -35.30, z-score =  -1.87, R)
>dp4.chr3 13014949 80 - 19779522
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUAUCG--------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).)))))).......-------- ( -29.80, z-score =  -2.23, R)
>droAna3.scaffold_12928 260993 83 - 771024
AUAAAGAUUUUUCUGCUGGGAAUCGAACCGACGAUCUUACGAUUUACAGGCAGAUAUCUU-AAUCAUUGAACCAUGGGGUCCUA-----------
...(((((...((((((..((((((..............))))))...)))))).)))))-.......(.(((....))).)..----------- ( -18.64, z-score =  -0.99, R)
>droEre2.scaffold_4929 15715912 80 - 26641161
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUGUCG--------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).)))))).......-------- ( -29.80, z-score =  -1.84, R)
>droYak2.chr2L 16215580 80 + 22324452
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUGUUG--------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).)))))).......-------- ( -29.80, z-score =  -1.87, R)
>droSec1.super_3 2338511 80 - 7220098
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUGUUG--------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).)))))).......-------- ( -29.80, z-score =  -1.87, R)
>droSim1.chr2L 6601146 80 - 22036055
------UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU-AUCCAUUAGGCCACUGGGGCAUGUUG--------
------...((((((.((((.......))))........((((((((((((....)))))-.....))))))).)))))).......-------- ( -29.80, z-score =  -1.87, R)
>consensus
______UUACCCCAGAUGGGACUCGAACCCACAAUCCCCGGCUUAGGAGGCCGAUGCCUU_AUCCAUUAGGCCACUGGGGCAUGUUG________
.........((((((.((((.......)))).......(((((.....)))))..((((.........))))..))))))............... (-23.46 = -21.27 +  -2.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:22:06 2011