Locus 7913

Sequence ID dm3.chr3L
Location 18,440,325 – 18,440,396
Length 71
Max. P 0.939994
window10892 window10893

overview

Window 2

Location 18,440,325 – 18,440,396
Length 71
Sequences 12
Columns 77
Reading direction forward
Mean pairwise identity 79.72
Shannon entropy 0.42533
G+C content 0.52725
Mean single sequence MFE -21.94
Consensus MFE -17.61
Energy contribution -17.39
Covariance contribution -0.21
Combinations/Pair 1.21
Mean z-score -1.39
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.936684
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18440325 71 + 24543557
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGUGAGGCACGUGACC---CGUGCCAGGUUUCCCUUGUUCU--
-.........((((.(((.....(((.(((((((......))))))).))---))))))))..............-- ( -23.80, z-score =  -1.56, R)
>droSim1.chr3L 17774559 71 + 22553184
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGUGAGGCACGUGACC---CGUGCCAGGUUUCCCUUGUUCU--
-.........((((.(((.....(((.(((((((......))))))).))---))))))))..............-- ( -23.80, z-score =  -1.56, R)
>droYak2.chr3L 8597342 71 - 24197627
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGGGAGGCACGUGACC---CGUGCCAGGUUUCCCUUGUUCU--
-.........((((.(((.....(((.(((((((......))))))).))---))))))))..............-- ( -23.80, z-score =  -1.20, R)
>droEre2.scaffold_4784 10311339 71 - 25762168
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGUGAGGCACGUGACC---CGUGCCAGGUUUCCCUUGUUCU--
-.........((((.(((.....(((.(((((((......))))))).))---))))))))..............-- ( -23.80, z-score =  -1.56, R)
>droAna3.scaffold_13337 4334784 71 - 23293914
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGGGAGGCACGUGGCC---CGUGCCAGGUUUCUCUUGUUCU--
-.........((((.(((.....(((.(((((((......))))))).))---))))))))..............-- ( -24.20, z-score =  -1.48, R)
>dp4.chrXR_group6 11337458 71 + 13314419
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCUGGGAGGCACGUGACU---CGGGCCAGGUUUCUCUUGUUCU--
-.........((((((.......(((.((((((((....)))))))).))---).))))))..............-- ( -24.40, z-score =  -2.14, R)
>droPer1.super_20 1237465 71 + 1872136
-CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCUGGGAGGCACGUGACU---CGGGCCAGGUUUCUCUUGUUCU--
-.........((((((.......(((.((((((((....)))))))).))---).))))))..............-- ( -24.40, z-score =  -2.14, R)
>droWil1.scaffold_180949 395133 55 + 6375548
-CACAAUUCGUUGGUCAUUAAAAGGGACACGUGCAUUGAAGCACGUGACC---GAGACC------------------
-...........((((.......((..(((((((......))))))).))---..))))------------------ ( -16.90, z-score =  -2.47, R)
>droSec1.super_19 435298 71 + 1257711
CAAAAACUCGCUGGUCAUUAGAAAGGACACGUGCAAUCUAGGACGUGGCC---CGUGCCAG-UUUUCCUUGUUCG--
.........(((((.(((......((.(((((.(......).)))))..)---))))))))-)............-- ( -16.80, z-score =  -0.21, R)
>droVir3.scaffold_13049 21636047 71 + 25233164
-CACAAUUCGUUGGUCAUUAAAAGGGACACGUGCAUUGAAGCACGUGACU---GAGGCCAGGUUCUC--GGCAUGGA
-.....(((((..(((........((.(((((((......))))))).))---((((......))))--)))))))) ( -18.40, z-score =  -0.31, R)
>droMoj3.scaffold_6680 16113789 74 + 24764193
-CACAAUUCGUUGGUCAUUAAAAGGGACACGUGCAUUGAAGCACGUGACCACCGAGGCCAGGUUCAC--GGCAUGGC
-.....((((.(((((((.....(.....)((((......))))))))))).))))((((.((....--.)).)))) ( -23.40, z-score =  -1.64, R)
>droGri2.scaffold_15110 2609545 73 - 24565398
-CACAAUUCGUUGGUCAUUAAAAGGGACACGUGCACUGGAGCACGUGACU---GAGGCCAGGUUCUCUCAACAUGGA
-........((((.........((((((((((((......))))))).((---(....)))..)))))))))..... ( -19.60, z-score =  -0.47, R)
>consensus
_CACAAUUCGCUGGUCAUUAAAAGGGACACGUGCAGUGAGGCACGUGACC___CGGGCCAGGUUUCCCUUGUUCU__
..........(((((.........((.(((((((......))))))).))......)))))................ (-17.61 = -17.39 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,440,325 – 18,440,396
Length 71
Sequences 12
Columns 77
Reading direction reverse
Mean pairwise identity 79.72
Shannon entropy 0.42533
G+C content 0.52725
Mean single sequence MFE -21.09
Consensus MFE -12.19
Energy contribution -11.98
Covariance contribution -0.21
Combinations/Pair 1.23
Mean z-score -2.06
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.939994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18440325 71 - 24543557
--AGAACAAGGGAAACCUGGCACG---GGUCACGUGCCUCACUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((((....))(((((.(---((.(((((((......))))))).)))......)).))).....)))).- ( -25.40, z-score =  -2.37, R)
>droSim1.chr3L 17774559 71 - 22553184
--AGAACAAGGGAAACCUGGCACG---GGUCACGUGCCUCACUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((((....))(((((.(---((.(((((((......))))))).)))......)).))).....)))).- ( -25.40, z-score =  -2.37, R)
>droYak2.chr3L 8597342 71 + 24197627
--AGAACAAGGGAAACCUGGCACG---GGUCACGUGCCUCCCUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((((....))(((((.(---((.(((((((......))))))).)))......)).))).....)))).- ( -25.40, z-score =  -2.36, R)
>droEre2.scaffold_4784 10311339 71 + 25762168
--AGAACAAGGGAAACCUGGCACG---GGUCACGUGCCUCACUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((((....))(((((.(---((.(((((((......))))))).)))......)).))).....)))).- ( -25.40, z-score =  -2.37, R)
>droAna3.scaffold_13337 4334784 71 + 23293914
--AGAACAAGAGAAACCUGGCACG---GGCCACGUGCCUCCCUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((.......((((((.(---((.(((((((......))))))).)))......)).))))....)))).- ( -21.80, z-score =  -2.13, R)
>dp4.chrXR_group6 11337458 71 - 13314419
--AGAACAAGAGAAACCUGGCCCG---AGUCACGUGCCUCCCAGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((.......(((((..(---((.(((((((......)))))))...))).....).))))....)))).- ( -16.10, z-score =  -1.44, R)
>droPer1.super_20 1237465 71 - 1872136
--AGAACAAGAGAAACCUGGCCCG---AGUCACGUGCCUCCCAGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG-
--...((((.......(((((..(---((.(((((((......)))))))...))).....).))))....)))).- ( -16.10, z-score =  -1.44, R)
>droWil1.scaffold_180949 395133 55 - 6375548
------------------GGUCUC---GGUCACGUGCUUCAAUGCACGUGUCCCUUUUAAUGACCAACGAAUUGUG-
------------------((((..---((.(((((((......))))))).))........))))...........- ( -19.80, z-score =  -3.99, R)
>droSec1.super_19 435298 71 - 1257711
--CGAACAAGGAAAA-CUGGCACG---GGCCACGUCCUAGAUUGCACGUGUCCUUUCUAAUGACCAGCGAGUUUUUG
--........(((((-((.((..(---(((.((((.(......).))))))))..((....))...)).))))))). ( -19.00, z-score =  -1.04, R)
>droVir3.scaffold_13049 21636047 71 - 25233164
UCCAUGCC--GAGAACCUGGCCUC---AGUCACGUGCUUCAAUGCACGUGUCCCUUUUAAUGACCAACGAAUUGUG-
..((((((--(......))))...---.(.(((((((......))))))).).......)))..............- ( -17.20, z-score =  -1.78, R)
>droMoj3.scaffold_6680 16113789 74 - 24764193
GCCAUGCC--GUGAACCUGGCCUCGGUGGUCACGUGCUUCAAUGCACGUGUCCCUUUUAAUGACCAACGAAUUGUG-
(((..(((--(......))))...)))((.(((((((......))))))).)).......................- ( -22.50, z-score =  -1.78, R)
>droGri2.scaffold_15110 2609545 73 + 24565398
UCCAUGUUGAGAGAACCUGGCCUC---AGUCACGUGCUCCAGUGCACGUGUCCCUUUUAAUGACCAACGAAUUGUG-
....(((((.(((........)))---.(.(((((((......))))))).)............))))).......- ( -19.00, z-score =  -1.62, R)
>consensus
__AGAACAAGGGAAACCUGGCACG___GGUCACGUGCCUCACUGCACGUGUCCCUUUUAAUGACCAGCGAAUUGUG_
.................((((......((.(((((((......)))))))...))......).)))........... (-12.19 = -11.98 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:35:53 2011