Locus 11656

Sequence ID dm3.chr3R
Location 22,773,221 – 22,773,351
Length 130
Max. P 0.999388
window16015 window16016

overview

Window 5

Location 22,773,221 – 22,773,351
Length 130
Sequences 14
Columns 142
Reading direction forward
Mean pairwise identity 67.14
Shannon entropy 0.71870
G+C content 0.42707
Mean single sequence MFE -32.63
Consensus MFE -22.03
Energy contribution -21.66
Covariance contribution -0.37
Combinations/Pair 1.39
Mean z-score -1.90
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.84
SVM RNA-class probability 0.999388
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22773221 130 + 27905053
---------AUUAAUUCGAGCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGAUACGAGCCACGCUGCUAAAUGACACUUUUGUGCUGCGGGCAC---
---------......(((..((((((((((((((.......)))))....((((((.....))))))...................))))))).))...)))(((.(((.((((((.......)))).)).))))))..--- ( -40.20, z-score =  -3.10, R)
>droSim1.chr3R 22604141 130 + 27517382
---------AUUAAUUUGAGAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGAUACGGAGCACGCUGCUAAAUGACACUUUUAUGUUGCGGGCAC---
---------...........((((((((((((((.......)))))....((((((.....))))))...................)))))))))........((.(((.((((((.......)))).)).))).))..--- ( -34.80, z-score =  -2.02, R)
>droSec1.super_14 1957689 105 + 2068291
-------------UUUAGUCUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCUCUAUGGGUGAUGAACGCCAAGAGG------------------------
-------------.....(((.(((....(((((.......))))).....((.((((((....)))))).))...((((((.((((((.....))))))))))))...))).)))..------------------------ ( -34.70, z-score =  -2.75, R)
>droYak2.chr3R 5119663 130 - 28832112
---------AUUAGUUACGGAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGAUAUGAGCCGUGCUGCCAAAUGACAGUUUUCUGCUGCGGGCAC---
---------...(((.((((((((((((((((((.......)))))....((((((.....))))))...................)))))))))........)))))))(((....(.((((.....))))).)))..--- ( -38.10, z-score =  -1.76, R)
>droEre2.scaffold_4820 5204169 130 - 10470090
---------GUUAAUUUGGGAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGAUAUGAAGCGUACUGCCAAAUGACACUUUUCUGCUGCGGGCAC---
---------((((.(((((.((((((((((((((.......)))))....((((((.....))))))...................)))))))))..((((...))))...))))))))).......(((.....))).--- ( -34.20, z-score =  -1.17, R)
>droAna3.scaffold_13340 7143420 128 - 23697760
---------AUUA-UUUUAGAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGGUGCCGGA-GAGCUGCUAAAGUACAAUUUUGUGCCACCGGCAC---
---------....-......((((((((((((((.......)))))....((((((.....))))))...................))))))))).(((((((.-(.((.((.(((......))).))))).)))))))--- ( -41.80, z-score =  -3.60, R)
>dp4.chr2 26119616 129 - 30794189
---------UUUUGUAAAUGCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGUUGGCGGACAG-CUGCUAAAACGCAAUUUUCAGCCAAAUGCGG---
---------.........((((((((((((((((.......)))))....((((((.....))))))...................)))))))...(((((.((.((-.(((......))).)).)).))))).)))).--- ( -38.30, z-score =  -2.34, R)
>droPer1.super_19 1496109 129 - 1869541
---------UUUUAUAAAUGCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGUUGUCGGACAG-CUGCUAAAACGCAAUUUUCAGCCAAAUGCGG---
---------..........(((((((((((((((.......)))))....((((((.....))))))...................)))))))..((((.....)))-)))).....((((.(((......))))))).--- ( -32.60, z-score =  -1.40, R)
>droWil1.scaffold_180708 913136 132 + 12563649
---------AUCUUCUUACUUAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCUAAAGCAAGA-GAUGAGCAAAGUUGUAUUUGAAGGCUAAAUGGCAUUU
---------((((.(((.(((.((((((((((((.......))))).....((.((((((....)))))).)).............)))))))...))).))))-)))...((((......))))...(((....))).... ( -33.90, z-score =  -0.98, R)
>droVir3.scaffold_13047 6362780 112 - 19223366
---------AAUAAUAAA--CAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCAGGUUGAAAAACGA-UUGCCAAAACAUAAUU------------------
---------.........--..((((((((((((.......)))))....((((((.....))))))...................)))))))..(((....)))..-................------------------ ( -26.50, z-score =  -2.83, R)
>droMoj3.scaffold_6540 28994094 112 + 34148556
---------AUUUAUUAA--CAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGAUGGGAAAUGU-UUGCCAAAACAUAGUU------------------
---------.((((((..--..((((((((((((.......)))))....((((((.....))))))...................)))))))..))))))..((((-((....))))))....------------------ ( -28.40, z-score =  -1.99, R)
>droGri2.scaffold_15074 1846061 112 + 7742996
---------AUUAGUUU--GAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCGUUAGGAAAUGU-CUGCCAAAACAUACUU------------------
---------....((((--((.((((((((((((.......)))))....((((((.....))))))...................)))))))))(.((((.....)-))).).))))......------------------ ( -26.90, z-score =  -1.39, R)
>anoGam1.chr3L 12834922 129 - 41284009
AUUGAUUCGUCGAUCUGCGGCAGGUUCCACCGAGAUUUGAACUCGGAUCGUUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUGGAACCUCGGUGAUGGAUGAAAGGCAGUUUUGCUAUUUGAAC-------------
.....((((((.(((.((.(.(((((((((((((.......)))))....((((((.....))))))...................))))))))).))))).)))))).(((......)))........------------- ( -40.70, z-score =  -1.79, R)
>triCas2.ChLG2 12682797 100 + 12900155
-------------------AAAGCUGCCUCCAAAAAUUCAAU--AAAAUAUAAAAUGUUCCAUUAAAAAAACAUAC-ACUGUAUUAUAGCUCAUUUCUGAAACACCU-GUAUAUUUUGAAAAU-------------------
-------------------......................(--((((((((...((((...........(((...-..)))........(((....)))))))...-.))))))))).....------------------- (  -5.70, z-score =   0.55, R)
>consensus
_________AUUAAUUAA_GAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGAUGCGAGACGA_CUGCCAAAUGACAAUUUU__GC_____GC_____
......................((((((((((((.......)))))....((((((.....))))))...................)))))))................................................. (-22.03 = -21.66 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,773,221 – 22,773,351
Length 130
Sequences 14
Columns 142
Reading direction reverse
Mean pairwise identity 67.14
Shannon entropy 0.71870
G+C content 0.42707
Mean single sequence MFE -31.69
Consensus MFE -22.87
Energy contribution -21.91
Covariance contribution -0.95
Combinations/Pair 1.61
Mean z-score -1.16
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.84
SVM RNA-class probability 0.995736
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22773221 130 - 27905053
---GUGCCCGCAGCACAAAAGUGUCAUUUAGCAGCGUGGCUCGUAUCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGCUCGAAUUAAU---------
---((((.....)))).........(((((((((.((.(((.(..(((((((((...(((((........)))))..)))))))))..).)))...(((((.......)))))....))))))).))))....--------- ( -37.60, z-score =  -1.25, R)
>droSim1.chr3R 22604141 130 - 27517382
---GUGCCCGCAACAUAAAAGUGUCAUUUAGCAGCGUGCUCCGUAUCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUCUCAAAUUAAU---------
---..((.(((....((((.......))))...))).))........(((((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))))...........--------- ( -30.20, z-score =  -0.62, R)
>droSec1.super_14 1957689 105 - 2068291
------------------------CCUCUUGGCGUUCAUCACCCAUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAGACUAAA-------------
------------------------((((((((.((.....))))).))))).....((((.((..((((....(.(((((.......))))).)..(((((.......)))))...)))))).))))..------------- ( -28.10, z-score =  -0.79, R)
>droYak2.chr3R 5119663 130 + 28832112
---GUGCCCGCAGCAGAAAACUGUCAUUUGGCAGCACGGCUCAUAUCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUCCGUAACUAAU---------
---.((((....((((....)))).....))))..((((........(((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))))).......--------- ( -36.30, z-score =  -1.14, R)
>droEre2.scaffold_4820 5204169 130 + 10470090
---GUGCCCGCAGCAGAAAAGUGUCAUUUGGCAGUACGCUUCAUAUCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUCCCAAAUUAAC---------
---.(((.....)))..........((((((.....((((.....(((((((((...(((((........)))))..)))))))))....))))..(((((.......)))))..........))))))....--------- ( -32.00, z-score =  -0.55, R)
>droAna3.scaffold_13340 7143420 128 + 23697760
---GUGCCGGUGGCACAAAAUUGUACUUUAGCAGCUC-UCCGGCACCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUCUAAAA-UAAU---------
---(((((((.(((.......(((......)))))).-.))))))).(((((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))))......-....--------- ( -40.61, z-score =  -2.87, R)
>dp4.chr2 26119616 129 + 30794189
---CCGCAUUUGGCUGAAAAUUGCGUUUUAGCAG-CUGUCCGCCAACAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGCAUUUACAAAA---------
---..((..(((((.((...((((......))))-...)).)))))..((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))..........--------- ( -39.80, z-score =  -2.32, R)
>droPer1.super_19 1496109 129 + 1869541
---CCGCAUUUGGCUGAAAAUUGCGUUUUAGCAG-CUGUCCGACAACAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGCAUUUAUAAAA---------
---..((.....(((((((......)))))))..-.............((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))..........--------- ( -33.50, z-score =  -0.76, R)
>droWil1.scaffold_180708 913136 132 - 12563649
AAAUGCCAUUUAGCCUUCAAAUACAACUUUGCUCAUC-UCUUGCUUUAGGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUAAGUAAGAAGAU---------
..................................(((-((((((((..((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))))))).))))--------- ( -36.00, z-score =  -1.61, R)
>droVir3.scaffold_13047 6362780 112 + 19223366
------------------AAUUAUGUUUUGGCAA-UCGUUUUUCAACCUGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUG--UUUAUUAUU---------
------------------......((((((...(-(((((.(((((...(((((...(((((........)))))..))))))))))...))))))(((((.......)))))))))))...--.........--------- ( -25.40, z-score =  -0.92, R)
>droMoj3.scaffold_6540 28994094 112 - 34148556
------------------AACUAUGUUUUGGCAA-ACAUUUCCCAUCGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUG--UUAAUAAAU---------
------------------......((..(((.((-....)).)))..))(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))..--.........--------- ( -26.10, z-score =  -0.80, R)
>droGri2.scaffold_15074 1846061 112 - 7742996
------------------AAGUAUGUUUUGGCAG-ACAUUUCCUAACGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUC--AAACUAAU---------
------------------.((((((((......)-))))........(((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))).--..)))...--------- ( -27.90, z-score =  -0.95, R)
>anoGam1.chr3L 12834922 129 + 41284009
-------------GUUCAAAUAGCAAAACUGCCUUUCAUCCAUCACCGAGGUUCCAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAACGAUCCGAGUUCAAAUCUCGGUGGAACCUGCCGCAGAUCGACGAAUCAAU
-------------.........(((....)))..(((.((.(((..((((((((((((((((........)))))((((((((.((.((....)))).))))))))......)))))))))..))..))).)).)))..... ( -33.40, z-score =  -0.90, R)
>triCas2.ChLG2 12682797 100 - 12900155
-------------------AUUUUCAAAAUAUAC-AGGUGUUUCAGAAAUGAGCUAUAAUACAGU-GUAUGUUUUUUUAAUGGAACAUUUUAUAUUUU--AUUGAAUUUUUGGAGGCAGCUUU-------------------
-------------------.((((((((((((((-(.((((((((....))).....)))))..)-))))))...((((((((((.........))))--))))))..)))))))).......------------------- ( -16.80, z-score =  -0.80, R)
>consensus
_____GC_____GC__AAAAUUGUCAUUUAGCAG_ACGUCUCCCAUCAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGC_UUAAUUAAU_________
................................................((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))..................... (-22.87 = -21.91 +  -0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:03 2011