Locus 9776

Sequence ID	dm3.chr3R
Location	8,847,040 – 8,847,132
Length	92
Max. P	0.843990

overview

Window 6

Location	8,847,040 – 8,847,132
Length	92
Sequences	13
Columns	98
Reading direction	forward
Mean pairwise identity	67.11
Shannon entropy	0.74571
G+C content	0.40239
Mean single sequence MFE	-16.74
Consensus MFE	-8.02
Energy contribution	-8.35
Covariance contribution	0.33
Combinations/Pair	1.15
Mean z-score	-0.36
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.16
SVM RNA-class probability	0.570657
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8847040 92 + 27905053
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGGCG-CCGCACCCACGAUGAAUGUGAUCG-CAACUAAUGAAUGUUUUCUUUU----
...(((((((.((((((.......))))))))))))).(((((.((-.((((..(.....)..))))..))-))))).................---- ( -18.00, z-score =   0.04, R)
>droAna3.scaffold_13340 14364248 90 - 23697760
AAGAGAUUGUUGUAAAACAAGGCAUUUUACGCAAUCUGAGUUGGCG-CCGCACCAACGUCGGCUAUGUUCU-UUAUUAACCAAUUGUUAAUU------
...(((((((.((((((.......))))))))))))).((((((((-.........)))))))).......-..((((((.....)))))).------ ( -19.30, z-score =  -0.54, R)
>droWil1.scaffold_181089 11583603 93 + 12369635
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUAGAAG-CCGCGCCUACACUGAACAAGAGACAUUACUAACCUAUU----ACCCCUUUA
...(((((((.((((((.......)))))))))))))..((((...-......))))............................----......... ( -12.30, z-score =  -0.64, R)
>droVir3.scaffold_12855 6192133 96 - 10161210
AAGAGAUUGUUGUAAAACGAAACAUUUUACGCAAUCUGAGACGACGACCCCGAC-ACGCUAGAUAUGUUUA-AUACUAAACAAAAUUAUUUUCCAAUU
...(((((((.((((((.......)))))))))))))((((...((....))..-..........((((((-....)))))).......))))..... ( -13.20, z-score =  -1.31, R)
>droGri2.scaffold_14906 7582597 93 - 14172833
AAGAGAUUGUUGUAAAACGAAACAUUUUACGCAAUCUGAGCAGACG-CAGCGACAGCGCUUGAUAUGUUUC-AUACUAAACGUUAUGUAUUCUUU---
...(((((((.((((((.......)))))))))))))..(((((((-.((((....))))(((......))-).......)))).))).......--- ( -17.80, z-score =   0.17, R)
>droMoj3.scaffold_6540 25872199 97 - 34148556
AAGAGAUUGUUGUAAAACGAAACAUUUUACGCAAUCUGAGACGAUGCCCGCAGUUGUGCUUGAUAUGUUUU-AUGCUAAUUGAAAUUCAUUUCGCAUU
...(((((((.((((((.......)))))))))))))((((.((......((((((.((.(((......))-).))))))))....)).))))..... ( -19.20, z-score =  -0.42, R)
>droPer1.super_0 9193191 95 + 11822988
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGACGACG-ACGCGCCAAUGUCGAGCACGUUCC-CUACUAACCUAUUUGUAAAACCUUU-
...(((((((.((((((.......)))))))))))))(..(((.((-(((......)))))....)))..)-.........................- ( -15.90, z-score =  -0.23, R)
>dp4.chr2 19471416 95 - 30794189
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGACGACG-ACGCGCCAAUGUCGAGCACGUUCC-CUACUAACCUAUUUGUAAAACCUUU-
...(((((((.((((((.......)))))))))))))(..(((.((-(((......)))))....)))..)-.........................- ( -15.90, z-score =  -0.23, R)
>droSim1.chr3R 14941723 92 - 27517382
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGGCG-CCGCACCCACGACGAAUGUGAUCG-CAACUAACCAAUGUUCUAUUUU----
...(((((((.((((((.......))))))))))))).(((((.((-.((((..(.....)..))))..))-))))).................---- ( -17.70, z-score =  -0.10, R)
>droSec1.super_0 7971115 92 - 21120651
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGGCG-CCGCACCCACGACGAAUGUGAUCG-CAACUAACCAAUGUUCUAUUUU----
...(((((((.((((((.......))))))))))))).(((((.((-.((((..(.....)..))))..))-))))).................---- ( -17.70, z-score =  -0.10, R)
>droYak2.chr3R 13142278 90 + 28832112
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGGCG-CCGCACCCACGUCGAAUGUGAUCG-CAACUAACCAGCGUUCUUUU------
...(((((((.((((((.......)))))))))))))..(((((..-..((...(((((...)))))...)-)......)))))........------ ( -18.90, z-score =   0.23, R)
>droEre2.scaffold_4770 4944803 90 - 17746568
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGGCG-CCGCACCCACGUCGAAUGUGAUCG-CAACUAACCAUCGUUCUUUU------
...(((((((.((((((.......))))))))))))).(((((.((-.((((..(.....)..))))..))-)))))...............------ ( -17.70, z-score =   0.36, R)
>apiMel3.GroupUn 7568196 72 + 399230636
--GGGUCAGUGCUCACAGUGUGAGUUUUAUCUAUCCAUAUCUAACCUUCUCUCACGUGAUUAAUGUUUUCCCUU------------------------
--(((.((.((.((((.(((.(((........................))).))))))).)).))....)))..------------------------ ( -14.06, z-score =  -1.83, R)
>consensus
AAGAGAUUGUUGUAAAACGAGACAUUUUACGCAAUCUGAGUUGACG_CCGCACCCACGUCGAAUAUGUUCC_CUACUAACCAAUGUUCUAUUC_____
...((((((.(((((((.......)))))))))))))............................................................. ( -8.02 =  -8.35 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	8,847,040 – 8,847,132
Length	92
Sequences	13
Columns	98
Reading direction	reverse
Mean pairwise identity	67.11
Shannon entropy	0.74571
G+C content	0.40239
Mean single sequence MFE	-20.20
Consensus MFE	-8.40
Energy contribution	-9.13
Covariance contribution	0.73
Combinations/Pair	1.28
Mean z-score	-1.02
Structure conservation index	0.42
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.88
SVM RNA-class probability	0.843990
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8847040 92 - 27905053
----AAAAGAAAACAUUCAUUAGUUG-CGAUCACAUUCAUCGUGGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
----..((((...........(((((-((.((.(((((.....))))).))-)).)))))..(((((.((((((((...))))))))..))))))))) ( -21.30, z-score =  -1.77, R)
>droAna3.scaffold_13340 14364248 90 + 23697760
------AAUUAACAAUUGGUUAAUAA-AGAACAUAGCCGACGUUGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGCCUUGUUUUACAACAAUCUCUU
------.........(((((((....-......))))))).(((((((...-)))))))..((((((.(((((((.....)))))))..))))))... ( -21.60, z-score =  -1.68, R)
>droWil1.scaffold_181089 11583603 93 - 12369635
UAAAGGGGU----AAUAGGUUAGUAAUGUCUCUUGUUCAGUGUAGGCGCGG-CUUCUACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
..(((((((----(((.(((.(((..((((((.........).)))))..)-))...)))...)))))((((((((...))))))))......))))) ( -19.10, z-score =  -0.88, R)
>droVir3.scaffold_12855 6192133 96 + 10161210
AAUUGGAAAAUAAUUUUGUUUAGUAU-UAAACAUAUCUAGCGU-GUCGGGGUCGUCGUCUCAGAUUGCGUAAAAUGUUUCGUUUUACAACAAUCUCUU
.((((...........((((((....-))))))......(((.-(((.(((.......))).))))))((((((((...))))))))..))))..... ( -14.00, z-score =   0.05, R)
>droGri2.scaffold_14906 7582597 93 + 14172833
---AAAGAAUACAUAACGUUUAGUAU-GAAACAUAUCAAGCGCUGUCGCUG-CGUCUGCUCAGAUUGCGUAAAAUGUUUCGUUUUACAACAAUCUCUU
---..............((((((.((-(((((((.....((((.(((...(-(....))...))).))))...))))))))).))).)))........ ( -19.80, z-score =  -1.07, R)
>droMoj3.scaffold_6540 25872199 97 + 34148556
AAUGCGAAAUGAAUUUCAAUUAGCAU-AAAACAUAUCAAGCACAACUGCGGGCAUCGUCUCAGAUUGCGUAAAAUGUUUCGUUUUACAACAAUCUCUU
.((((((((....)))).........-............(((....)))..))))......((((((.((((((((...))))))))..))))))... ( -16.00, z-score =  -0.42, R)
>droPer1.super_0 9193191 95 - 11822988
-AAAGGUUUUACAAAUAGGUUAGUAG-GGAACGUGCUCGACAUUGGCGCGU-CGUCGUCUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
-........................(-((((((((((.......)))))))-.....))))((((((.((((((((...))))))))..))))))... ( -20.50, z-score =  -0.40, R)
>dp4.chr2 19471416 95 + 30794189
-AAAGGUUUUACAAAUAGGUUAGUAG-GGAACGUGCUCGACAUUGGCGCGU-CGUCGUCUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
-........................(-((((((((((.......)))))))-.....))))((((((.((((((((...))))))))..))))))... ( -20.50, z-score =  -0.40, R)
>droSim1.chr3R 14941723 92 + 27517382
----AAAAUAGAACAUUGGUUAGUUG-CGAUCACAUUCGUCGUGGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
----...........(((((..((((-((..(((.......)))..)))))-))))))...((((((.((((((((...))))))))..))))))... ( -24.50, z-score =  -1.85, R)
>droSec1.super_0 7971115 92 + 21120651
----AAAAUAGAACAUUGGUUAGUUG-CGAUCACAUUCGUCGUGGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
----...........(((((..((((-((..(((.......)))..)))))-))))))...((((((.((((((((...))))))))..))))))... ( -24.50, z-score =  -1.85, R)
>droYak2.chr3R 13142278 90 - 28832112
------AAAAGAACGCUGGUUAGUUG-CGAUCACAUUCGACGUGGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
------..((((....((((..((((-((..(((.......)))..)))))-))))).....(((((.((((((((...))))))))..))))))))) ( -24.10, z-score =  -0.99, R)
>droEre2.scaffold_4770 4944803 90 + 17746568
------AAAAGAACGAUGGUUAGUUG-CGAUCACAUUCGACGUGGGUGCGG-CGCCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
------..((((....((((..((((-((..(((.......)))..)))))-))))).....(((((.((((((((...))))))))..))))))))) ( -24.30, z-score =  -1.16, R)
>apiMel3.GroupUn 7568196 72 - 399230636
------------------------AAGGGAAAACAUUAAUCACGUGAGAGAAGGUUAGAUAUGGAUAGAUAAAACUCACACUGUGAGCACUGACCC--
------------------------...............((.(....).)).((((((.(((......)))...(((((...)))))..)))))).-- ( -12.40, z-score =  -0.80, R)
>consensus
_____GAAUAAAACAUUGGUUAGUAG_CGAACAUAUUCGACGUGGGUGCGG_CGUCAACUCAGAUUGCGUAAAAUGUCUCGUUUUACAACAAUCUCUU
............................................((((....)))).....((((((.((((((((...))))))))..))))))... ( -8.40 =  -9.13 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:10:50 2011