Locus 7206

Sequence ID dm3.chr3L
Location 12,985,981 – 12,986,232
Length 251
Max. P 0.942495
window9916 window9917 window9918

overview

Window 6

Location 12,985,981 – 12,986,083
Length 102
Sequences 11
Columns 117
Reading direction forward
Mean pairwise identity 74.57
Shannon entropy 0.49591
G+C content 0.39280
Mean single sequence MFE -19.30
Consensus MFE -9.31
Energy contribution -9.07
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -1.82
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.92
SVM RNA-class probability 0.852260
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12985981 102 + 24543557
UUCGGAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCC---------------CUUGCUUGGCUCAGCUUAGCCAGAGUCCUUCGAA
.(((((....((..(((((((....)))))))..)).(((((.....)))))...........(((..---------------((.(((.(((...))).))).)).))).))))). ( -23.30, z-score =  -1.75, R)
>droPer1.super_9 2647229 89 + 3637205
UCCGGCUCCUUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGUGCAAUAUUUCAAAGAACCC---------------CACCCUGGACCCCACAUCGUC-------------
...((.((((((..(((((((....)))))))..)))(((((.....)))))................---------------......))).)).........------------- ( -15.80, z-score =  -1.94, R)
>dp4.chrXR_group6 4358078 89 + 13314419
UCCGACUCCUUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGUGCAAUAUUUCAAAGAACCC---------------CACCCUGGACCCCACAUCGUC-------------
((((.....(((..(((((((....)))))))..)))(((((.....)))))................---------------.....))))............------------- ( -13.10, z-score =  -1.93, R)
>droAna3.scaffold_13337 6520964 117 - 23293914
UCCGUCUCCUUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGUGCAAUAUUUCAAAGGACCCAGCCCAGUACAUGACUCUGCUUAGCUCAGCUUAGCCAAUGUCCUUUGAG
.........(((..(((((((....)))))))..)))(((((.....))))).....(((((((((..(((..(((.....)))..)))..(((......)))....))))))))). ( -26.90, z-score =  -2.33, R)
>droEre2.scaffold_4784 12992396 102 + 25762168
UCCUGCUUCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAUUUCAAACGACUC---------------CAUGCUUAGCUCAACUUAGCCAGAGUCCUUCGAA
..........((..(((((((....)))))))..)).(((((.....)))))....(((.((.(((((---------------...(((.((.....)).)))..))))).)).))) ( -21.20, z-score =  -2.44, R)
>droYak2.chr3L 13063704 102 + 24197627
UCCUGCUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAUUUCAACCGACUC---------------CUUGCUUAGCUCAGCUCAGCCAGAGUCCUUCGAU
..........((..(((((((....)))))))..)).(((((.....)))))...........(((((---------------...(((.(((...))).)))..)))))....... ( -22.90, z-score =  -2.46, R)
>droSec1.super_0 5157621 102 + 21120651
UUCGUAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCC---------------UUUGCUUGGCUCAGCUUAGCCAGAGUCCUUCGAA
.((((.....((..(((((((....)))))))..)).(((((.....))))).........))))...---------------...((((((((......))))).)))........ ( -21.50, z-score =  -1.68, R)
>droSim1.chr3L 12368806 102 + 22553184
UUCGUAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCC---------------CUUGCUUGGCUCAGCUUAGCCAGAGUCCUUCGAA
.((((.....((..(((((((....)))))))..)).(((((.....))))).........))))...---------------...((((((((......))))).)))........ ( -21.50, z-score =  -1.75, R)
>droVir3.scaffold_13049 2718683 100 - 25233164
UCCUGGUCACCAUUUAAUUAAGCACUUAAUUAUUUAAUGUG-UGAUUGCGCAAUAUUUCAAACGUAGC---------------CUUCG-CUCGUCUACUUAAUGACAACUCAUCCAA
....(((((((((((((((((....)))))))...)))).)-)))))................(.(((---------------....)-)))(((........)))........... ( -14.80, z-score =  -0.97, R)
>droMoj3.scaffold_6680 7636824 102 - 24764193
UCCUGGUCUCCGUUUAAUUAAGUACUUAAUUAUUUAAUGCGCUGAUUGUGCAAUAUUUCAAACGUUGC---------------CUUCAACUCGUCUGCUUAAUGACAACUCAUCCAA
....(((...(((((.((((((((......))))))))((((.....))))........)))))..))---------------)........(((........)))........... ( -17.50, z-score =  -2.07, R)
>droGri2.scaffold_15110 21026165 101 + 24565398
UCCUGGUCGCCAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGUGCAAUAUUUCAAACGUAUC---------------CUUUG-CUCCUCGACUUAAUGACAACUCAUCCAA
...(((..........(((((((..............(((((.....)))))...........(((..---------------...))-).....).))))))..........))). ( -13.85, z-score =  -0.71, R)
>consensus
UCCGGCUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAUUUCAAACGACCC_______________CUUGCUUGGCUCAGCUUAGCCAGAGUCCUUCGAA
..............(((((((....))))))).....(((((.....)))))................................................................. ( -9.31 =  -9.07 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,986,083 – 12,986,232
Length 149
Sequences 5
Columns 178
Reading direction forward
Mean pairwise identity 67.37
Shannon entropy 0.55948
G+C content 0.34634
Mean single sequence MFE -33.76
Consensus MFE -14.14
Energy contribution -14.26
Covariance contribution 0.12
Combinations/Pair 1.24
Mean z-score -1.63
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.748693
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12986083 149 + 24543557
AGUUAGCUAUAAAGUGGACCAUAGUAGUGACAGAUAAAAUGAACUGGACCUUAA-----------UUGUUAACGAAUAAAAUG-GGUAGUAAGAUGAUUACGAAAACACGCUGUGAAAAUGUAAUAUAAUUAG-----------------CUUCUGCUCUAGAAGGUCCACCCUAAAA
.............((((((((((((.(((.(((..........))).((((...-----------(((((....)))))...)-))).((((.....)))).....)))))))))..................-----------------((((((...))))))))))))....... ( -29.30, z-score =  -0.91, R)
>droEre2.scaffold_4784 12992498 164 + 25762168
UUUGAGCUAUAAAGUGGACCUCAGUAGUGGCACACUUAGUGAACUGUACCCCAAACGUUUGCUUUUUGAUAAAGUAUAAAGU-----AAUUUGUAAAAUAUGAAUACACUCUGUGAACAUUUGAUUUAAAUAUCCCUAAC---------GUAUUUAAGCUAUAGGGUCCACCCUAAAA
.............((((((((((.(((((...))).)).))).(((((...((((.(((..(...((.(((...((((((..-----..))))))...))).))........)..))).)))).(((((((((.......---------))))))))).))))))))))))....... ( -33.30, z-score =  -0.85, R)
>droYak2.chr3L 13063806 155 + 24197627
UGUGAGCUAUAAAGUGGACCCAAGUAGUGACAGAUUCAAUAAAGAAAACCCCAAUGUUUUGCUCUUUGUUUGAUUACAAAAAGGAAGAAUAUGUAAAAUAAGAAUGCACCCAGUGAAAAC---GUUUAAGCUGC--------------------UGCUCUAUAAGGUCCACCCUAAAA
.............(((((((...((((.(.(((.....................(((((((((((((.(((........))).)))))....)))))))).....((.....((....))---......))..)--------------------))).))))..)))))))....... ( -31.00, z-score =  -1.45, R)
>droSec1.super_0 5157723 166 + 21120651
AGUGAGCUAUAGAGUGGACCAUAGUAGUGACAGAUAAAAUGAACUGGACCUUAA-----------UUGUUAACGAAUAAAAUG-AAUAGUAAGAAGUUUACGAAAACACCCAGUGAAAAUUUAAUUUAAUUAGGCCAGACUUCAUUUUAGCUUCCGCUCUAGAAGGUCCACCCUAGAA
.........(((.(((((((.(((.((((..((.(((((((((((((.(((.((-----------(((...............-....(((((...))))).....(((...)))...........))))))))))))..))))))))).))..)))))))...))))))).)))... ( -41.80, z-score =  -3.60, R)
>droSim1.chr3L 12368908 166 + 22553184
AGUGAGCUAUAAAGUGGACCAUAGUAGUGACAGAAAAAAUUAACUGGACCUUUA-----------UUGUUAACGAAUAAAACG-AAUAGUAAGAAGAUUACGAAAACAGCUUGUGAAAAUGUAAUUUAAUUAGGCCAGAUUUCAUUUAUGCUUCCGCUUUAGAAGGUCCACCCUAGAA
.(((..((.(((((((((.(((((((((..........)))).((((.((((((-----------(((((..((.......))-))))))))..((((((((...((.....)).....))))))))....))))))).......)))))..)))))))))...))..)))....... ( -33.40, z-score =  -1.35, R)
>consensus
AGUGAGCUAUAAAGUGGACCAUAGUAGUGACAGAUAAAAUGAACUGGACCUUAA___________UUGUUAACGAAUAAAAUG_AAUAGUAAGAAGAUUACGAAAACACCCUGUGAAAAUGUAAUUUAAUUAGCCC__A__________GCUUCUGCUCUAGAAGGUCCACCCUAAAA
.............(((((((.(((.((((...........................................................((((.....)))).....(((...))).......................................)))))))...)))))))....... (-14.14 = -14.26 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,986,083 – 12,986,232
Length 149
Sequences 5
Columns 178
Reading direction reverse
Mean pairwise identity 67.37
Shannon entropy 0.55948
G+C content 0.34634
Mean single sequence MFE -34.54
Consensus MFE -16.18
Energy contribution -16.50
Covariance contribution 0.32
Combinations/Pair 1.19
Mean z-score -1.84
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942495
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12986083 149 - 24543557
UUUUAGGGUGGACCUUCUAGAGCAGAAG-----------------CUAAUUAUAUUACAUUUUCACAGCGUGUUUUCGUAAUCAUCUUACUACC-CAUUUUAUUCGUUAACAA-----------UUAAGGUCCAGUUCAUUUUAUCUGUCACUACUAUGGUCCACUUUAUAGCUAACU
...(((((((((((...(((.(((((.(-----------------((...................))).((((..((................-.........))..)))).-----------....................)))))..)))....)))))))))))......... ( -25.52, z-score =  -0.78, R)
>droEre2.scaffold_4784 12992498 164 - 25762168
UUUUAGGGUGGACCCUAUAGCUUAAAUAC---------GUUAGGGAUAUUUAAAUCAAAUGUUCACAGAGUGUAUUCAUAUUUUACAAAUU-----ACUUUAUACUUUAUCAAAAAGCAAACGUUUGGGGUACAGUUCACUAAGUGUGCCACUACUGAGGUCCACUUUAUAGCUCAAA
...((((((((((((..(((((.....((---------(((..((((((((.....))))))))..((((((((.....(((.....))).-----....))))))))...........)))))..))((((((.((....)).)))))).)))..).)))))))))))......... ( -39.70, z-score =  -2.28, R)
>droYak2.chr3L 13063806 155 - 24197627
UUUUAGGGUGGACCUUAUAGAGCA--------------------GCAGCUUAAAC---GUUUUCACUGGGUGCAUUCUUAUUUUACAUAUUCUUCCUUUUUGUAAUCAAACAAAGAGCAAAACAUUGGGGUUUUCUUUAUUGAAUCUGUCACUACUUGGGUCCACUUUAUAGCUCACA
...((((((((((((..(((....--------------------(((.((.....---.........)).)))...........(((.((((...((((((((......)))))))).(((((......))))).......)))).)))..)))...))))))))))))......... ( -34.34, z-score =  -1.36, R)
>droSec1.super_0 5157723 166 - 21120651
UUCUAGGGUGGACCUUCUAGAGCGGAAGCUAAAAUGAAGUCUGGCCUAAUUAAAUUAAAUUUUCACUGGGUGUUUUCGUAAACUUCUUACUAUU-CAUUUUAUUCGUUAACAA-----------UUAAGGUCCAGUUCAUUUUAUCUGUCACUACUAUGGUCCACUCUAUAGCUCACU
...(((((((((((...(((((.(..((.(((((((((..(((((((((((...((((.........(((((.....((((.....))))....-)))))......)))).))-----------)).))).))))))))))))).))..).)).))).)))))))))))......... ( -42.06, z-score =  -3.33, R)
>droSim1.chr3L 12368908 166 - 22553184
UUCUAGGGUGGACCUUCUAAAGCGGAAGCAUAAAUGAAAUCUGGCCUAAUUAAAUUACAUUUUCACAAGCUGUUUUCGUAAUCUUCUUACUAUU-CGUUUUAUUCGUUAACAA-----------UAAAGGUCCAGUUAAUUUUUUCUGUCACUACUAUGGUCCACUUUAUAGCUCACU
...(((((((((((.......(((((((...((((.....(((((((..............................((((.....))))....-.(((.........)))..-----------...))).))))...))))))))))).........)))))))))))......... ( -31.09, z-score =  -1.43, R)
>consensus
UUUUAGGGUGGACCUUCUAGAGCAGAAGC__________U__GGCCUAAUUAAAUUAAAUUUUCACAGGGUGUUUUCGUAAUCUUCUUACUAUU_CAUUUUAUUCGUUAACAA___________UUAAGGUCCAGUUCAUUUUAUCUGUCACUACUAUGGUCCACUUUAUAGCUCACU
...(((((((((((...(((.(((((.....................................(((...))).....((((.....))))......................................................)))).).)))....)))))))))))......... (-16.18 = -16.50 +   0.32)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:28 2011