Locus 5706

Sequence ID dm3.chr3L
Location 598,823 – 598,959
Length 136
Max. P 0.911608
window7837 window7838

overview

Window 7

Location 598,823 – 598,927
Length 104
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 61.51
Shannon entropy 0.66500
G+C content 0.38120
Mean single sequence MFE -28.90
Consensus MFE -6.42
Energy contribution -5.65
Covariance contribution -0.77
Combinations/Pair 1.57
Mean z-score -2.65
Structure conservation index 0.22
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.885151
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 598823 104 - 24543557
----UAUUUGGCAAUUCCAGUUACUUCUGGAUUUGCCGAAUACAAAUACA---AAUACAAA--CAUUAACUAAAUAGUGUAUCGUGGAGUGGAUCGAUUUCUUGGUAUUAGAA
----((((((((((.(((((......))))).))))))))))........---(((((..(--(((((......))))))..((.(((((......))))).))))))).... ( -28.40, z-score =  -3.57, R)
>droEre2.scaffold_4784 601050 103 - 25762168
----UAUUUGACAAUUCCAGGCACUUGUGGAGUUGCCAAAUACAAAUUAA----AUACUAA--CAUUAACUAAAUAGUGUACCGUGGAGUGGAUCGAUUUCUUGGUAUGCAAA
----((((((.((((((((.(....).)))))))).))))))........----.......--.............((((((((.(((((......))))).))))))))... ( -26.40, z-score =  -2.31, R)
>droYak2.chr3L 581403 111 - 24197627
CACGUACUUGACAAUUCCAGUUACUUCUGGAGUUGCCAAGUACAAAUUAAUUAGAUACUAG--CAUUAACUAAAUAGUGUAUCGUGGAGUGGAUCGAUUUCUUGGUAUGUAAA
...(((((((.(((((((((......))))))))).))))))).......(((.(((((((--(((((......)))))).....(((((......))))).)))))).))). ( -34.80, z-score =  -4.19, R)
>droSim1.chr3L 248404 103 - 22553184
----UAUUUGGCAACUCCAGUUGCUUUUGGAUUUGCCAAACACAAAU-UA---AAUGCUAA--CAUUAACUAAAUAGUGUAUCGUGGAGUGGAUCGAUUUCUUGGUAUUAAAA
----..((((((((.(((((......))))).)))))))).......-..---((((((((--(((((......)))))).....(((((......))))).))))))).... ( -25.60, z-score =  -2.49, R)
>dp4.chrXR_group3a 698996 99 + 1468910
------UUCAAGGACACC-----CUUGUGCCUUGUGCGUACGCAGAUCUUCCUGGGAGCAGCCCGGGAAAUAAAUAUUAUUUUGCGAUGUGUAUAAACAGUUUCUCGUGC---
------..(((((.(((.-----...))))))))...(((((.(((..((((((((.....))))))))..................(((......)))...))))))))--- ( -29.10, z-score =  -1.68, R)
>droPer1.super_23 860091 99 + 1662726
------AUCAAGGACACC-----CUUGUGCCUUGUGCGUACGCAGAUCUUCCUGGGAGCAGCCCGGGAAAUAAAUAUUAUUUUGCGAUGUGUAUAAACAGUUUCUCGUGC---
------..(((((.(((.-----...))))))))...(((((.(((..((((((((.....))))))))..................(((......)))...))))))))--- ( -29.10, z-score =  -1.68, R)
>consensus
____UAUUUGACAACUCCAGUUACUUGUGGAUUUGCCAAACACAAAUCUA___GAUACUAA__CAUUAACUAAAUAGUGUAUCGUGGAGUGGAUCGAUUUCUUGGUAUGCAAA
...........................(((.....)))........................................((((((.(((((......))))).))))))..... ( -6.42 =  -5.65 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 598,852 – 598,959
Length 107
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 53.95
Shannon entropy 0.80026
G+C content 0.37628
Mean single sequence MFE -28.24
Consensus MFE 0.00
Energy contribution 0.00
Covariance contribution 0.00
Combinations/Pair 0.00
Mean z-score -3.78
Structure conservation index -0.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911608
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 598852 107 - 24543557
ACUUUCCAUGGUACCCAGAAAGCUUAAAAUAUUAUUUGGCAAUUCCAGUUACUUCUG-GAUUUGC-CGAAUACAAAUACA---AAUACAAA--CAUUAACUAAAUAGUGUAUCG
.(((((..(((...))))))))..........((((((((((.(((((......)))-)).))))-))))))........---.......(--(((((......)))))).... ( -27.30, z-score =  -4.99, R)
>droEre2.scaffold_4784 601079 90 - 25762168
---------ACUUUCCAUUUAAUAU-------UAUUUGACAAUUCCAGGCACUUGUG-GAGUUGC-CAAAUACAAAUUAA----AUACUAA--CAUUAACUAAAUAGUGUACCG
---------.......(((((((..-------((((((.((((((((.(....).))-)))))).-))))))...)))))----))....(--(((((......)))))).... ( -19.70, z-score =  -3.61, R)
>droYak2.chr3L 581432 100 - 24197627
---------ACUUUCAUUAUAAUAUCUCAC-GUACUUGACAAUUCCAGUUACUUCUG-GAGUUGC-CAAGUACAAAUUAAUUAGAUACUAG--CAUUAACUAAAUAGUGUAUCG
---------.....................-(((((((.(((((((((......)))-)))))).-)))))))..........(((((...--...............))))). ( -27.17, z-score =  -5.28, R)
>droSim1.chr3L 248433 106 - 22553184
ACUUUCCAUGGUGCCCAGAAAGCUUAAAAUAUUAUUUGGCAACUCCAGUUGCUUUUG-GAUUUGC-CAAACACAAAU-UA---AAUGCUAA--CAUUAACUAAAUAGUGUAUCG
.(((((..(((...))))))))............((((((((.(((((......)))-)).))))-)))).......-..---.......(--(((((......)))))).... ( -22.90, z-score =  -2.02, R)
>dp4.chrXR_group3a 699022 103 + 1468910
-----------AUUUCCGUUCGCUCGCAGGAAUCUCCAGACUUCAAGGACACCCUUGUGCCUUGUGCGUACGCAGAUCUUCCUGGGAGCAGCCCGGGAAAUAAAUAUUAUUUUG
-----------.((((((..(((((.((((((..((.......(((((.(((....))))))))(((....)))))..)))))).)))).)..))))))............... ( -36.20, z-score =  -3.37, R)
>droPer1.super_23 860117 103 + 1662726
-----------AUUUCCGUUCGCUCGCAGGAAUCUCCAGACAUCAAGGACACCCUUGUGCCUUGUGCGUACGCAGAUCUUCCUGGGAGCAGCCCGGGAAAUAAAUAUUAUUUUG
-----------.((((((..(((((.((((((..((.......(((((.(((....))))))))(((....)))))..)))))).)))).)..))))))............... ( -36.20, z-score =  -3.38, R)
>consensus
___________UUUCCAGAUAGCUUAAAAGAAUAUUUGGCAAUUCCAGUCACUUUUG_GACUUGC_CAAACACAAAUCUA___GAUACUAA__CAUUAACUAAAUAGUGUAUCG
.................................................................................................................. (  0.00 =   0.00 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:53:31 2011