Locus 11995

Sequence ID dm3.chr3R
Location 24,998,157 – 24,998,264
Length 107
Max. P 0.999978
window16484 window16485

overview

Window 4

Location 24,998,157 – 24,998,264
Length 107
Sequences 11
Columns 117
Reading direction forward
Mean pairwise identity 62.11
Shannon entropy 0.78030
G+C content 0.55882
Mean single sequence MFE -27.75
Consensus MFE -10.52
Energy contribution -9.79
Covariance contribution -0.73
Combinations/Pair 1.55
Mean z-score -1.68
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977919
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24998157 107 + 27905053
----GAUCUGCAGCCUAUGUACCAUUCGACCUUUGCAUUGGACAGACCCGCAAAUCUUCCCCUAUUUUCGGCUAGCCCAAUGCACUGCCCGAAAAUCCUC--GGCC-CGACCAG---
----....((((.....))))....(((.....((((((((.(((..(((.((((........)))).))))).).))))))))....((((......))--))..-)))....--- ( -21.20, z-score =  -0.86, R)
>droPer1.super_7 2003855 116 + 4445127
GAUCAUCUUUCAGCGGGCACCG-CUUCGAACUCUGCAUUGGACAGACCCGAAAAUCUUCCCCUAUUCCCGGCUAGCCCAAUGCACAAUCCCAGGUCCCCCCCGGCCACGAUCCCGAU
((((....((((((((...)))-))..)))...((((((((.(((..(((..(((........)))..))))).).))))))))........((((......))))..))))..... ( -27.10, z-score =  -0.31, R)
>dp4.chr2 1840333 116 + 30794189
GAUCAUCUUUCAGCGGGCACCG-CUUCGAACUCUGCAUUGGACAGACCCGAAAAUCUUCCCCUAUUCCCGGCUAGCCCAAUGCACAAUCCCAGGUCCCCCCCGGCCUCGAUCCCGAU
((((....((((((((...)))-))..)))...((((((((.(((..(((..(((........)))..))))).).)))))))).......(((((......))))).))))..... ( -27.20, z-score =  -0.20, R)
>droAna3.scaffold_13340 9453822 101 - 23697760
---GAUCCUCCGGCCGGCGAGGACUUCAAACUCCGCAUUGGACAGACCCGAAAAUCUUCCCCUAUUCUCGACUAGCCCAAUACCCAAUUCGAAAGCCA----GACCUC---------
---.....((.(((...((((((........)))..(((((.(((...(((.(((........))).))).)).).))))).......)))...))).----))....--------- ( -15.50, z-score =   1.12, R)
>droEre2.scaffold_4820 7438451 103 - 10470090
----GAUCAGCAGCCU----ACCAUUCGGCCUACGCAUUGGACAGACCCGGAAAUCUUCCCCUACUUCCGGCUAGCCCAGUGCACUGCCCGAAAAUCCUC--GGCC-CGAUCUG---
----((((.((((((.----.......)))....(((((((.(((..((((((............)))))))).).)))))))..)))((((......))--))..-.))))..--- ( -32.40, z-score =  -3.04, R)
>droYak2.chr3R 7332031 106 - 28832112
----GAUCUGCAGCCUUCG-GCCAUUCGGCCACCGCAUUGGACAGACCCGGAAAUCUUCCCCUAUUCCCGGCUAGCCCAGUGCACUGCCCGAAAAUCCUU--GGCC-CGAUCUG---
----((((.((((.....(-(((....))))...(((((((.(((.((.((((...........)))).)))).).))))))).))))((((......))--))..-.))))..--- ( -36.10, z-score =  -2.92, R)
>droSec1.super_4 3862640 107 + 6179234
----GAUCUGCAGCCGAUGUACCAUUCGGCCUUCGCAUUGGACAGACCCGCAAAUCUUCCCCUAUUUCCGGCUAGCCCAAUGCACUGCCCGAAAAUCCUC--GGCC-CGACCAG---
----.....((((((((........)))))....(((((((.(((..(((.((((........)))).))))).).)))))))..)))((((......))--))..-.......--- ( -28.00, z-score =  -1.77, R)
>droSim1.chr3R 24669728 107 + 27517382
----GAUCUGCAGCCGAUGCACCAUUCGGCCUUCGCAUUGGACAGACCCGCAAAUCUUCCCCUACUUCCGGCUAGCCCAAUGCACUGCCCGAAAAUCCUC--GGCC-CGACCAG---
----.....((((((((........)))))....(((((((.(((.((.....................)))).).)))))))..)))((((......))--))..-.......--- ( -25.40, z-score =  -0.81, R)
>droVir3.scaffold_12822 2265766 96 + 4096053
----UGUUCUUGGCCAGCCAAA-UGUGAG-CUCAGCACUGGAC-GCACGAAGAAUCUUCCCCUAUUAUUGGCUCGCCCAGUGCUCAGC-CCCGGCCGACCAUUC-------------
----.....((((((.((....-.))..(-((.((((((((..-((..((((...)))).((.......))...)))))))))).)))-...))))))......------------- ( -29.40, z-score =  -1.38, R)
>droMoj3.scaffold_6540 26400197 97 + 34148556
----UAUUUGCGGUCAGCUUAA-UGUGAA-CUCAGCACGGGAC-GCUCUAAGAAUCUUCCCCUAUUCUUAGCCCGCCCCAUGCUGAGUUCUCAAUCAACCAUUU-------------
----.....((.....))....-((.(((-(((((((.(((.(-(..((((((((........))))))))..)).))).)))))))))).))...........------------- ( -35.60, z-score =  -6.25, R)
>droGri2.scaffold_14624 3200422 107 + 4233967
----UAUAACUGAUCAGCU-AA-UGUGAGGCUCAGCACUGGAC-GCACUAAGAAUCUUCCCCUAUUAUUGGCUCGCCCAGUGCUCAACUUCAAAGAUAUCAGACCGACCGAUUC---
----.....(((((...((-..-..(((((...((((((((.(-(..((((.(((........))).))))..)).))))))))...))))).))..)))))............--- ( -27.40, z-score =  -2.00, R)
>consensus
____GAUCUGCAGCCGGCG_AC_AUUCGGCCUCCGCAUUGGACAGACCCGAAAAUCUUCCCCUAUUCCCGGCUAGCCCAAUGCACAGCCCGAAAACCCUC__GGCC_CGAUC_G___
..................................(((((((.(....(((..................)))...).))))))).................................. (-10.52 =  -9.79 +  -0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 24,998,157 – 24,998,264
Length 107
Sequences 11
Columns 117
Reading direction reverse
Mean pairwise identity 62.11
Shannon entropy 0.78030
G+C content 0.55882
Mean single sequence MFE -44.88
Consensus MFE -26.00
Energy contribution -24.35
Covariance contribution -1.65
Combinations/Pair 1.87
Mean z-score -3.40
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 5.56
SVM RNA-class probability 0.999978
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24998157 107 - 27905053
---CUGGUCG-GGCC--GAGGAUUUUCGGGCAGUGCAUUGGGCUAGCCGAAAAUAGGGGAAGAUUUGCGGGUCUGUCCAAUGCAAAGGUCGAAUGGUACAUAGGCUGCAGAUC----
---..((((.-((((--...(((((((((.(..((((((((((.(.(((.((((........)))).))).)..))))))))))..).))))).))).)...))))...))))---- ( -37.10, z-score =  -1.93, R)
>droPer1.super_7 2003855 116 - 4445127
AUCGGGAUCGUGGCCGGGGGGGACCUGGGAUUGUGCAUUGGGCUAGCCGGGAAUAGGGGAAGAUUUUCGGGUCUGUCCAAUGCAGAGUUCGAAG-CGGUGCCCGCUGAAAGAUGAUC
.....((((((...(((.(((.((((.(((((.((((((((((.(.(((..(((........)))..))).)..)))))))))).))))).)..-.))).))).)))....)))))) ( -50.20, z-score =  -3.20, R)
>dp4.chr2 1840333 116 - 30794189
AUCGGGAUCGAGGCCGGGGGGGACCUGGGAUUGUGCAUUGGGCUAGCCGGGAAUAGGGGAAGAUUUUCGGGUCUGUCCAAUGCAGAGUUCGAAG-CGGUGCCCGCUGAAAGAUGAUC
.....(((((....(((.(((.((((.(((((.((((((((((.(.(((..(((........)))..))).)..)))))))))).))))).)..-.))).))).))).....))))) ( -48.60, z-score =  -2.76, R)
>droAna3.scaffold_13340 9453822 101 + 23697760
---------GAGGUC----UGGCUUUCGAAUUGGGUAUUGGGCUAGUCGAGAAUAGGGGAAGAUUUUCGGGUCUGUCCAAUGCGGAGUUUGAAGUCCUCGCCGGCCGGAGGAUC---
---------..((.(----(((((((((((((..(((((((((.(.((((((((........)))))))).)..)))))))))..))))))))).....)))))))........--- ( -37.30, z-score =  -1.58, R)
>droEre2.scaffold_4820 7438451 103 + 10470090
---CAGAUCG-GGCC--GAGGAUUUUCGGGCAGUGCACUGGGCUAGCCGGAAGUAGGGGAAGAUUUCCGGGUCUGUCCAAUGCGUAGGCCGAAUGGU----AGGCUGCUGAUC----
---..(((((-((((--.......(((((.(..((((.(((((.(.((((((((........)))))))).)..))))).))))..).)))))....----.)))..))))))---- ( -44.20, z-score =  -2.81, R)
>droYak2.chr3R 7332031 106 + 28832112
---CAGAUCG-GGCC--AAGGAUUUUCGGGCAGUGCACUGGGCUAGCCGGGAAUAGGGGAAGAUUUCCGGGUCUGUCCAAUGCGGUGGCCGAAUGGC-CGAAGGCUGCAGAUC----
---..((((.-((((--..((...(((((.((.((((.(((((.(.((((((((........)))))))).)..))))).)))).)).)))))...)-)...))))...))))---- ( -49.70, z-score =  -3.69, R)
>droSec1.super_4 3862640 107 - 6179234
---CUGGUCG-GGCC--GAGGAUUUUCGGGCAGUGCAUUGGGCUAGCCGGAAAUAGGGGAAGAUUUGCGGGUCUGUCCAAUGCGAAGGCCGAAUGGUACAUCGGCUGCAGAUC----
---..((((.-((((--((..((((((((.(..((((((((((.(.(((.((((........)))).))).)..))))))))))..).))))).)))...))))))...))))---- ( -45.90, z-score =  -3.44, R)
>droSim1.chr3R 24669728 107 - 27517382
---CUGGUCG-GGCC--GAGGAUUUUCGGGCAGUGCAUUGGGCUAGCCGGAAGUAGGGGAAGAUUUGCGGGUCUGUCCAAUGCGAAGGCCGAAUGGUGCAUCGGCUGCAGAUC----
---..((((.-((((--(((.((((((((.(..((((((((((.(.(((.((((........)))).))).)..))))))))))..).))))).))).).))))))...))))---- ( -46.70, z-score =  -3.16, R)
>droVir3.scaffold_12822 2265766 96 - 4096053
-------------GAAUGGUCGGCCGGG-GCUGAGCACUGGGCGAGCCAAUAAUAGGGGAAGAUUCUUCGUGC-GUCCAGUGCUGAG-CUCACA-UUUGGCUGGCCAAGAACA----
-------------...((((((((((((-(((.(((((((((((..((........))((((...))))...)-)))))))))).))-)))...-..))))))))))......---- ( -49.00, z-score =  -5.05, R)
>droMoj3.scaffold_6540 26400197 97 - 34148556
-------------AAAUGGUUGAUUGAGAACUCAGCAUGGGGCGGGCUAAGAAUAGGGGAAGAUUCUUAGAGC-GUCCCGUGCUGAG-UUCACA-UUAAGCUGACCGCAAAUA----
-------------....((((...((.(((((((((((((((((..((((((((........))))))))..)-)))))))))))))-))).))-...))))...........---- ( -47.20, z-score =  -7.24, R)
>droGri2.scaffold_14624 3200422 107 - 4233967
---GAAUCGGUCGGUCUGAUAUCUUUGAAGUUGAGCACUGGGCGAGCCAAUAAUAGGGGAAGAUUCUUAGUGC-GUCCAGUGCUGAGCCUCACA-UU-AGCUGAUCAGUUAUA----
---.....((((((.(((((.....(((.(((.(((((((((((.((......((((((....)))))))).)-)))))))))).))).))).)-))-)))))))).......---- ( -37.80, z-score =  -2.57, R)
>consensus
___C_GAUCG_GGCC__GAGGAUUUUCGGGCUGUGCAUUGGGCUAGCCGGGAAUAGGGGAAGAUUUUCGGGUCUGUCCAAUGCGGAGGCCGAAU_GU_CGCCGGCUGCAGAUC____
.........................((((.(..((((((((((...((((((((........))))))))....))))))))))..).))))......................... (-26.00 = -24.35 +  -1.65)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:38 2011