Locus 12063

Sequence ID dm3.chr3R
Location 25,373,265 – 25,373,340
Length 75
Max. P 0.975391
window16582 window16583

overview

Window 2

Location 25,373,265 – 25,373,340
Length 75
Sequences 12
Columns 77
Reading direction forward
Mean pairwise identity 94.13
Shannon entropy 0.12846
G+C content 0.38090
Mean single sequence MFE -18.57
Consensus MFE -16.64
Energy contribution -16.73
Covariance contribution 0.09
Combinations/Pair 1.05
Mean z-score -2.17
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952499
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25373265 75 + 27905053
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUCUUAACGGCUAG--
.........((((((.((((.....)))).(((((.((((((...)))))).)))))...........)))))).-- ( -19.30, z-score =  -2.53, R)
>droSim1.chr3R 25046455 75 + 27517382
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUCUUAACGGCUAG--
.........((((((.((((.....)))).(((((.((((((...)))))).)))))...........)))))).-- ( -19.30, z-score =  -2.53, R)
>droSec1.super_4 4231504 75 + 6179234
CGUGUUCAUUAGCCACCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGACGUCUUAACGGCUAG--
.........(((((..((((.....)))).(((((.((((((...)))))).)))))............))))).-- ( -18.00, z-score =  -2.50, R)
>droYak2.chr3R 7726613 75 - 28832112
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUCUUAACGGCUAG--
.........((((((.((((.....)))).(((((.((((((...)))))).)))))...........)))))).-- ( -19.30, z-score =  -2.53, R)
>droEre2.scaffold_4820 7841322 74 - 10470090
-CUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUCUUAACGGCUAA--
-.......(((((((.((((.....)))).(((((.((((((...)))))).)))))...........)))))))-- ( -19.50, z-score =  -2.90, R)
>droAna3.scaffold_12911 5067740 75 + 5364042
GGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGCUUUAACGGCUAG--
.........((((((.((((.....)))).(((((.((((((...)))))).)))))...........)))))).-- ( -19.30, z-score =  -1.98, R)
>dp4.chr2 2241511 77 + 30794189
CGGGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCAUUUUAACGGCUCGAG
..........(((((.((((.....)))).(((((.((((((...)))))).)))))...........))))).... ( -17.30, z-score =  -1.51, R)
>droPer1.super_7 2406338 77 + 4445127
CGGGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCAUUUUAACGGCUCGAG
..........(((((.((((.....)))).(((((.((((((...)))))).)))))...........))))).... ( -17.30, z-score =  -1.51, R)
>droWil1.scaffold_181089 5624781 75 + 12369635
CGUGUUCAUUAGCUGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUUUUAACGGCUAG--
(((((..((((.......))))..))))).(((((.((((((...)))))).)))))((((((....))))))..-- ( -18.20, z-score =  -2.07, R)
>droVir3.scaffold_12855 705520 75 + 10161210
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAAUAUAUUUAUUGAAUGUUUUGGCAGGCGUUUUAACGGCUCG--
..........((((((((((.....)))..(((((.((((((...)))))).))))).)))((....))))))..-- ( -18.10, z-score =  -1.43, R)
>droMoj3.scaffold_6540 21884923 75 - 34148556
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGCCGUUUUAACGGCUCA--
(((((..((((.......))))..))))).(((((.((((((...)))))).)))))((((((....))))))..-- ( -20.30, z-score =  -2.70, R)
>droGri2.scaffold_14906 1809573 75 + 14172833
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAACCAACAUAUUUAUUGAAUGUUUUGGCAGUCGCUUUAACGGCUAG--
.........(((((....((((..(((((......)))))..))))...(((..(((....)))..)))))))).-- ( -16.90, z-score =  -1.83, R)
>consensus
CGUGUUCAUUAGCCGCCAUAAUUUAUAUGAGCCAACAUAUUUAUUGAAUGUUUUGGCAGUCGUUUUAACGGCUAG__
..........(((((.((((.....)))).(((((.((((((...)))))).)))))...........))))).... (-16.64 = -16.73 +   0.09)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 25,373,265 – 25,373,340
Length 75
Sequences 12
Columns 77
Reading direction reverse
Mean pairwise identity 94.13
Shannon entropy 0.12846
G+C content 0.38090
Mean single sequence MFE -17.15
Consensus MFE -15.53
Energy contribution -15.54
Covariance contribution 0.02
Combinations/Pair 1.11
Mean z-score -2.36
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.93
SVM RNA-class probability 0.975391
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25373265 75 - 27905053
--CUAGCCGUUAAGACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--.(((((((..........((((..((((.........)))))))).((((.....)))))))))))......... ( -18.20, z-score =  -2.89, R)
>droSim1.chr3R 25046455 75 - 27517382
--CUAGCCGUUAAGACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--.(((((((..........((((..((((.........)))))))).((((.....)))))))))))......... ( -18.20, z-score =  -2.89, R)
>droSec1.super_4 4231504 75 - 6179234
--CUAGCCGUUAAGACGUCUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGUGGCUAAUGAACACG
--.((((((...........((((..((((.........))))))))(((((.....)))))))))))......... ( -15.30, z-score =  -1.52, R)
>droYak2.chr3R 7726613 75 + 28832112
--CUAGCCGUUAAGACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--.(((((((..........((((..((((.........)))))))).((((.....)))))))))))......... ( -18.20, z-score =  -2.89, R)
>droEre2.scaffold_4820 7841322 74 + 10470090
--UUAGCCGUUAAGACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACAG-
--((((((((..........((((..((((.........)))))))).((((.....)))))))))))).......- ( -18.80, z-score =  -3.13, R)
>droAna3.scaffold_12911 5067740 75 - 5364042
--CUAGCCGUUAAAGCGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACC
--.(((((((..........((((..((((.........)))))))).((((.....)))))))))))......... ( -18.20, z-score =  -2.45, R)
>dp4.chr2 2241511 77 - 30794189
CUCGAGCCGUUAAAAUGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACCCG
....((((((((.(((....((((..((((.........))))))))........))).)))))))).......... ( -17.30, z-score =  -2.37, R)
>droPer1.super_7 2406338 77 - 4445127
CUCGAGCCGUUAAAAUGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACCCG
....((((((((.(((....((((..((((.........))))))))........))).)))))))).......... ( -17.30, z-score =  -2.37, R)
>droWil1.scaffold_181089 5624781 75 - 12369635
--CUAGCCGUUAAAACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCAGCUAAUGAACACG
--...(((((..........((((..((((.........))))))))...........))))).............. ( -13.10, z-score =  -1.47, R)
>droVir3.scaffold_12855 705520 75 - 10161210
--CGAGCCGUUAAAACGCCUGCCAAAACAUUCAAUAAAUAUAUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--..((((((..........(((((.................))))).((((.....)))))))))).......... ( -15.23, z-score =  -1.68, R)
>droMoj3.scaffold_6540 21884923 75 + 34148556
--UGAGCCGUUAAAACGGCUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--..((((((....))))))(((........(((((....)))))((.((((.....)))))))))........... ( -20.10, z-score =  -2.97, R)
>droGri2.scaffold_14906 1809573 75 - 14172833
--CUAGCCGUUAAAGCGACUGCCAAAACAUUCAAUAAAUAUGUUGGUUCAUAUAAAUUAUGGCGGCUAAUGAACACG
--.(((((((..........((((..((((.........)))))))).((((.....)))))))))))......... ( -15.90, z-score =  -1.67, R)
>consensus
__CUAGCCGUUAAAACGACUGCCAAAACAUUCAAUAAAUAUGUUGGCUCAUAUAAAUUAUGGCGGCUAAUGAACACG
....((((((..........((((..((((.........)))))))).((((.....)))))))))).......... (-15.53 = -15.54 +   0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:59 2011