Locus 6025

Sequence ID dm3.chr3L
Location 3,135,767 – 3,135,905
Length 138
Max. P 0.671870
window8291 window8292

overview

Window 1

Location 3,135,767 – 3,135,870
Length 103
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 86.03
Shannon entropy 0.23554
G+C content 0.45681
Mean single sequence MFE -33.30
Consensus MFE -24.82
Energy contribution -27.10
Covariance contribution 2.28
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.671870
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3135767 103 + 24543557
CGUUGCGAAUUUUUGGUUU--------GGUUUGCUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCCGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA--UUCAAAUGGGAA
((((..(((((((((((((--------((....))))....((((((.((....(((((((((((...))))))))))).)).)))))).)).))))))--))).)))).... ( -39.70, z-score =  -3.11, R)
>droEre2.scaffold_4784 3144389 89 + 25762168
CGUUGCGAAUUUUUGGUUU--------GGUUUGCUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUC----------------CGCAGGACACGCAAAAAAUUUUAAAUGGCCA
..(((((.....(((((..--------.....)))))....((((((.((..((((.....)))))----------------)))))))..)))))................. ( -19.60, z-score =   0.59, R)
>droYak2.chr3L 15390348 110 - 24197627
CGUUGCGAAUUUCUGGUUUUCUGGUUUGGUUUGCUAAUUAAUCUUGCCGGUCAUGGGUAAUCCAUCUGAUGGGUUGCCC--CCGCAGGACACGCAAAAAAUUU-AAAUGGCCA
..(((((...(((((.....(((((..((((........))))..)))))....(((((((((((...)))))))))))--...)))))..))))).......-......... ( -33.90, z-score =  -1.36, R)
>droSec1.super_2 3129262 102 + 7591821
CGUUGCGAAUUUUUGGUUU--------GGUUUGCUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAA---UUUAAAUGGGAA
..(((((.....(((((..--------.....)))))....((((((.((....(((((((((((...))))))))))).)).))))))..)))))..---............ ( -36.10, z-score =  -2.55, R)
>droSim1.chr3L 2663284 103 + 22553184
CGUUGCGAAUUUUUGGUUU--------GGUUUGCUAAUUAAUCUUGCCGGCCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA--UUUAAAUGGGAA
((((..(((((((((((((--------((....))))....((((((.((....(((((((((((...))))))))))).)).)))))).)).))))))--))).)))).... ( -37.20, z-score =  -2.44, R)
>consensus
CGUUGCGAAUUUUUGGUUU________GGUUUGCUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA__UUUAAAUGGGAA
..(((((.....(((((...............)))))....((((((.((....((((((((((.....))))))))))..))))))))..)))))................. (-24.82 = -27.10 +   2.28)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 3,135,792 – 3,135,905
Length 113
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 88.09
Shannon entropy 0.20850
G+C content 0.51296
Mean single sequence MFE -38.48
Consensus MFE -30.50
Energy contribution -31.86
Covariance contribution 1.36
Combinations/Pair 1.17
Mean z-score -1.59
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.566271
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3135792 113 + 24543557
CUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCCGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA--UUCAAAUGGGAAAAAGGUUGGCAGGGUCAAGUUGGGGGCCACUCAGG
((((((.(((((((((..(..(((((((((((...)))))))))))(((((...((..........--.))...)))))....)..)))))))))..))))))............ ( -41.50, z-score =  -1.86, R)
>droEre2.scaffold_4784 3144414 99 + 25762168
CUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUC----------------CGCAGGACACGCAAAAAAUUUUAAAUGGCCAAAAGGUUGGCAAGGUCAAGUUGGGGGCCACUCAGG
........((((((.((..((((.....)))))----------------)))))))..................(((((...((.(((((...))))).))...)))))...... ( -25.80, z-score =  -0.33, R)
>droYak2.chr3L 15390381 112 - 24197627
CUAAUUAAUCUUGCCGGUCAUGGGUAAUCCAUCUGAUGGGUUGCC--CCCGCAGGACACGCAAAAAAUUU-AAAUGGCCAAAUGGCUGGCGAGGUCAAGUUGGGGGCCACUCAGG
((((((.(((((((((((((((((((((((((...))))))))))--)..((.......)).........-..........))))))))))))))..))))))............ ( -40.70, z-score =  -1.69, R)
>droSec1.super_2 3129287 112 + 7591821
CUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAA---UUUAAAUGGGAAAAAGGUUGGCAGGGUCAAGUUGGGGGCCACUCAGG
((((((.(((((((((..(..(((((((((((...)))))))))))((((((.......))...(---(....))))))....)..)))))))))..))))))............ ( -40.10, z-score =  -1.65, R)
>droSim1.chr3L 2663309 113 + 22553184
CUAAUUAAUCUUGCCGGCCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA--UUUAAAUGGGAAAAAGGUUGGCAGGGUCAAGUUGGGGGCCACUCAGU
((((((.((((((((((((..(((((((((((...)))))))))))((((((.......))....(--(....))))))....))))))))))))..))))))............ ( -44.30, z-score =  -2.43, R)
>consensus
CUAAUUAAUCUUGCCGGUCAUGGGCAAUCCAUCUGAUGGGUUGCCCUCCCGCAGGACACGCAAAAA__UUUAAAUGGGAAAAAGGUUGGCAGGGUCAAGUUGGGGGCCACUCAGG
((((((.((((((((((((..((((((((((.....))))))))))....((.......))......................))))))))))))..))))))............ (-30.50 = -31.86 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:59:51 2011