Locus 6869

Sequence ID dm3.chr3L
Location 10,358,332 – 10,358,406
Length 74
Max. P 0.998488
window9449 window9450

overview

Window 9

Location 10,358,332 – 10,358,406
Length 74
Sequences 15
Columns 89
Reading direction forward
Mean pairwise identity 85.48
Shannon entropy 0.31396
G+C content 0.42503
Mean single sequence MFE -31.80
Consensus MFE -30.19
Energy contribution -30.41
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -6.44
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.67
SVM RNA-class probability 0.994048
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10358332 74 + 24543557
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUU--CAUUAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((..--.........--------..))))))))))..))))).))))..))). ( -32.32, z-score =  -6.96, R)
>droGri2.scaffold_15110 12043374 76 - 24565398
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUAAAUUUAAAUA--------CUCAUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((.(.............--------..).))))))))..))))).))))..))). ( -26.46, z-score =  -5.20, R)
>droMoj3.scaffold_6680 4142271 76 - 24764193
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAAUUUAAAUA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.90, R)
>droVir3.scaffold_13049 16143990 76 + 25233164
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAAUUUAUAUA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.93, R)
>droWil1.scaffold_181024 1528994 76 - 1751709
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUUUAAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.90, R)
>droPer1.super_27 1191224 76 + 1201981
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUAUUAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.85, R)
>dp4.chrXR_group6 8756412 76 + 13314419
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUAUUAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.85, R)
>droAna3.scaffold_13337 15274257 76 + 23293914
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUAACAUUAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.............--------..))))))))))..))))).))))..))). ( -32.16, z-score =  -6.82, R)
>droEre2.scaffold_4784 10353140 74 + 25762168
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUU--CAUUAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((..--.........--------..))))))))))..))))).))))..))). ( -32.32, z-score =  -6.96, R)
>droYak2.chr3L 10348890 74 + 24197627
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAU--UAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.....--......--------..))))))))))..))))).))))..))). ( -32.32, z-score =  -6.96, R)
>droSec1.super_0 2571170 74 + 21120651
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAU--UAUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((.....--......--------..))))))))))..))))).))))..))). ( -32.32, z-score =  -6.96, R)
>droSim1.chr3L 9747999 74 + 22553184
-----UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUU--AUAAA--------CUCGUAGGAACUUCAUACCGUGCUCUUGGA
-----......(((..((((.(((((..((((((((((......--.....--------..))))))))))..))))).))))..))). ( -32.32, z-score =  -6.96, R)
>triCas2.ChLG3 18613783 78 - 32080666
UUUUUGGUAGACCACUAGCGAGGUAUAGAGUUCCUACGUGAUUUUUCGGCU-----------GUAGGAACUUCAUACCGUGCUCUUGGA
...........(((..((((.(((((..(((((((((((((....)))..)-----------)))))))))..))))).))))..))). ( -31.90, z-score =  -4.71, R)
>anoGam1.chr2L 18352302 78 + 48795086
-----------CCACCAGCGAGGUAUAGAGUUCCUAUGUGCCCACUAGGCCGUUCGCUACUCAUAGGAACUUCAUACCGUGCUCUUGGA
-----------(((..((((.(((((..((((((((((.(((.....))).((.....)).))))))))))..))))).))))..))). ( -33.10, z-score =  -4.68, R)
>apiMel3.Group7 4171611 67 + 9974240
-----------CCAGCAGCGAGGUAUAGAGUUCCUACGUAGUGUUCAGAAAGU-----------AGGAACUUCAUACCGUGCUCUUGGA
-----------((((.((((.(((((..(((((((((..............))-----------)))))))..))))).)))).)))). ( -30.94, z-score =  -5.95, R)
>consensus
_____UUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUUUUAUAAA________CUCGUAGGAACUUCAUACCGUGCUCUUGGA
...........(((..((((.(((((..((((((((((.......................))))))))))..))))).))))..))). (-30.19 = -30.41 +   0.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,358,332 – 10,358,406
Length 74
Sequences 15
Columns 89
Reading direction reverse
Mean pairwise identity 85.48
Shannon entropy 0.31396
G+C content 0.42503
Mean single sequence MFE -28.38
Consensus MFE -26.54
Energy contribution -26.64
Covariance contribution 0.10
Combinations/Pair 1.09
Mean z-score -5.42
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.38
SVM RNA-class probability 0.998488
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10358332 74 - 24543557
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUAAUG--AACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------.........--..)))))))))).))))))..)))..)))......----- ( -28.02, z-score =  -5.48, R)
>droGri2.scaffold_15110 12043374 76 + 24565398
UCCAAGAGCACGGUAUGAAGUUCCUAUGAG--------UAUUUAAAUUUAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------((........)).)))))))))).))))))..)))..)))......----- ( -26.30, z-score =  -5.11, R)
>droMoj3.scaffold_6680 4142271 76 + 24764193
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UAUUUAAAUUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------((.......))..)))))))))).))))))..)))..)))......----- ( -29.00, z-score =  -5.85, R)
>droVir3.scaffold_13049 16143990 76 - 25233164
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UAUAUAAAUUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------((.......))..)))))))))).))))))..)))..)))......----- ( -29.00, z-score =  -6.00, R)
>droWil1.scaffold_181024 1528994 76 + 1751709
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUUAAAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.(((((((((..(--------(((((...))))))))))))))).))))))..)))..)))......----- ( -28.80, z-score =  -5.77, R)
>droPer1.super_27 1191224 76 - 1201981
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUAAUAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.(((((((((..(--------(((((...))))))))))))))).))))))..)))..)))......----- ( -28.80, z-score =  -5.77, R)
>dp4.chrXR_group6 8756412 76 - 13314419
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUAAUAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.(((((((((..(--------(((((...))))))))))))))).))))))..)))..)))......----- ( -28.80, z-score =  -5.77, R)
>droAna3.scaffold_13337 15274257 76 - 23293914
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUAAUGUUAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------.(((......))))))))))))).))))))..)))..)))......----- ( -27.90, z-score =  -5.21, R)
>droEre2.scaffold_4784 10353140 74 - 25762168
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUAAUG--AACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------.........--..)))))))))).))))))..)))..)))......----- ( -28.02, z-score =  -5.48, R)
>droYak2.chr3L 10348890 74 - 24197627
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUA--AUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------......--.....)))))))))).))))))..)))..)))......----- ( -28.02, z-score =  -5.48, R)
>droSec1.super_0 2571170 74 - 21120651
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAUA--AUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------......--.....)))))))))).))))))..)))..)))......----- ( -28.02, z-score =  -5.48, R)
>droSim1.chr3L 9747999 74 - 22553184
UCCAAGAGCACGGUAUGAAGUUCCUACGAG--------UUUAU--AAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA-----
.(((..(((..((((((.((((((((((..--------.....--......)))))))))).))))))..)))..)))......----- ( -28.02, z-score =  -5.48, R)
>triCas2.ChLG3 18613783 78 + 32080666
UCCAAGAGCACGGUAUGAAGUUCCUAC-----------AGCCGAAAAAUCACGUAGGAACUCUAUACCUCGCUAGUGGUCUACCAAAAA
.(((..(((..((((((.(((((((((-----------..............))))))))).))))))..)))..)))........... ( -27.74, z-score =  -5.35, R)
>anoGam1.chr2L 18352302 78 - 48795086
UCCAAGAGCACGGUAUGAAGUUCCUAUGAGUAGCGAACGGCCUAGUGGGCACAUAGGAACUCUAUACCUCGCUGGUGG-----------
.(((..(((..((((((.((((((((((.((.....)).(((.....))).)))))))))).))))))..)))..)))----------- ( -33.70, z-score =  -4.04, R)
>apiMel3.Group7 4171611 67 - 9974240
UCCAAGAGCACGGUAUGAAGUUCCU-----------ACUUUCUGAACACUACGUAGGAACUCUAUACCUCGCUGCUGG-----------
.(((..(((..((((((.(((((((-----------((..............))))))))).))))))..)))..)))----------- ( -25.54, z-score =  -5.06, R)
>consensus
UCCAAGAGCACGGUAUGAAGUUCCUACGAG________UUUAUAAAAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAA_____
.(((..(((..((((((.((((((((((.......................)))))))))).))))))..)))..)))........... (-26.54 = -26.64 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:15:59 2011