Locus 1829

Sequence ID dm3.chr2L
Location 14,206,002 – 14,206,140
Length 138
Max. P 0.895105
window2514 window2515

overview

Window 4

Location 14,206,002 – 14,206,108
Length 106
Sequences 9
Columns 110
Reading direction forward
Mean pairwise identity 63.09
Shannon entropy 0.79479
G+C content 0.46311
Mean single sequence MFE -25.05
Consensus MFE -10.23
Energy contribution -10.40
Covariance contribution 0.17
Combinations/Pair 1.76
Mean z-score -1.04
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.895105
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14206002 106 + 23011544
UUUCUCGAUUGCUGUU-GCACCUGAGCCGAGGAAAUCCCGC---AUGAAAAACUAUUUGGGGAGUGUUUUUUAUUGCGCUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
..........(((..(-(((((.(.((((.((....)))..---............(((((((((((........)))))))))))))).)..))))))...)))..... ( -31.20, z-score =  -1.36, R)
>droWil1.scaffold_180708 1263894 105 + 12563649
--CCUCAAAACUAAGCCAAAGCAAAAAAUACACCAACGC-CAACAACAACAACAACUUGAAAUGCAUUUGGCAAGCAGCCUCUCGAGAAUCGUUUUGGUAGUAGUUUU--
--....(((((((.((((((((...............((-(((...((.(((....)))...))...))))).......((....))....))))))))..)))))))-- ( -19.60, z-score =  -1.29, R)
>droPer1.super_16 1533472 108 + 1990440
CUUCUCGAGUGUUGCUCGUACCUGAACAAAAUCCCCCCCACCCCAUGGAAAACUGUUUGGAAA-UGUAUUUUAUUACACUCUUCAAGGCACACACCACACCACAUCGCU-
......(.((((((((.....(..((((...(((............)))....))))..)...-((((......))))........)))).))))).............- ( -15.40, z-score =   0.40, R)
>dp4.chr4_group4 1168059 108 - 6586962
CUUCUCGAGUGUUGCUCGUACCUGAACAAAAUCCCCCCCACCCCAUGGAAAACUGUUUGGAAA-UGUAUUUUAUUACACUCUUCAAGGCACACACCACACCACAUCGCU-
......(.((((((((.....(..((((...(((............)))....))))..)...-((((......))))........)))).))))).............- ( -15.40, z-score =   0.40, R)
>droAna3.scaffold_12916 4601183 83 - 16180835
CUCCUCCAA-GCCGAU-GCACCUGAGC----GAAAUCCCAU---ACGGAAAACUAUU-AAAGAGUGUAUUUUACGGCGCCCUUCA-GGCCCAAG----------------
.........-((((((-((((((....----....(((...---..)))........-..)).))))))....))))(((.....-))).....---------------- ( -17.17, z-score =  -0.82, R)
>droEre2.scaffold_4929 15379657 94 - 26641161
UUUCUCGAGUGCUGUU-GCACCUGGGCCGAGGAAA---------------AACUAUUUGGGGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
......((((...((.-(((((.(((((.((....---------------..))..(((((((((((........)))))))))))))).)).)))))))...))))... ( -34.20, z-score =  -3.02, R)
>droYak2.chr2L 14304227 106 + 22324452
UUUUUCGAGUGCUGUG-GCACCUGAGUCGAGGAAAUCCCGC---ACGAAAAACUAUUUGGGGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
(((((((.((((....-))))....(.((.((....)))))---.)))))))....(((((((((((........)))))))))))(((((.....)))))......... ( -33.10, z-score =  -1.73, R)
>droSec1.super_3 463578 106 + 7220098
UUUCUCGAGUGCUGUU-GCACCUGAGCCGAGGAAAUCCCGC---ACGAAAAACUAUUUGGCGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
........((((....-)))).(((((.(.((....)))((---(((........(((((.((((((........)))))).)))))........)))))...))))).. ( -29.69, z-score =  -0.99, R)
>droSim1.chr2L 13949307 106 + 22036055
UUUCUCGAGUGCUGUU-GCACCUGAGCCGAGGAAAUCCCGC---ACGAAAAACUAUUUGGCGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
........((((....-)))).(((((.(.((....)))((---(((........(((((.((((((........)))))).)))))........)))))...))))).. ( -29.69, z-score =  -0.99, R)
>consensus
UUUCUCGAGUGCUGUU_GCACCUGAGCCGAGGAAAUCCCGC___ACGAAAAACUAUUUGGAGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUAAGCUUAUG
.........((((....((......)).............................(((((((((((........))))))))))))))).................... (-10.23 = -10.40 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 14,206,037 – 14,206,140
Length 103
Sequences 9
Columns 113
Reading direction forward
Mean pairwise identity 63.34
Shannon entropy 0.75489
G+C content 0.42607
Mean single sequence MFE -21.65
Consensus MFE -10.00
Energy contribution -10.27
Covariance contribution 0.26
Combinations/Pair 1.75
Mean z-score -0.50
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.635792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14206037 103 + 23011544
---------CCCGCAUGAAAAACUAUUUGGGGAGUGUUUUUUAUUGCGCUCUUCAAGGCACCUGGUGUGCUA-AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
---------((((((((........((((((((((((........))))))))))))........)))))..-(((......)))..........)))............... ( -26.69, z-score =  -1.17, R)
>droWil1.scaffold_180708 1263921 109 + 12563649
ACACCAACGCCAACAACAACAACAACUUGAAAUGCAUUUGGCAAGCAGCCUCUCGAGAAUCGUUUUG-GUAGUAGUUUUUCCUUUAGCCUUGUCAUGAGUGAAACAAAAA---
.(((((..(((((...((.(((....)))...))...)))))..((.(((...((.....))....)-)).))......................)).))).........--- ( -14.10, z-score =   2.31, R)
>droPer1.super_16 1533504 109 + 1990440
--CCCCCCCACCCCAUGGAAAACUGUUUGGA-AAUGUAUUUUAUUACACUCUUCAAGGCACACACCACACCACAUCGCUCCUUCUACUAAGCUCAGGGACAA-AUAAAAUUGC
--.........(((.(((........(((((-..((((......))))...)))))((......))...)))....(((..........)))...)))....-.......... ( -13.50, z-score =   1.19, R)
>dp4.chr4_group4 1168091 109 - 6586962
--CCCCCCCACCCCAUGGAAAACUGUUUGGA-AAUGUAUUUUAUUACACUCUUCAAGGCACACACCACACCACAUCGCUCCUUCCACUAAGCUCAGGGACAA-AUAAAAUUGC
--.........(((.(((........(((((-..((((......))))...)))))((......))...)))....(((..........)))...)))....-.......... ( -13.50, z-score =   1.29, R)
>droAna3.scaffold_12916 4601213 92 - 16180835
---------CCCAUACGGAAAACUAUU-AAAGAGUGUAUUUUACGGCGCCCUUCAGGC--CCAAGUGUUCCA-ACAUUUCAGGGACAAAAUAGCGCAAAGAGCGC--------
---------(((....((((.(((...-.....(((.....)))((.(((.....)))--)).))).)))).-........)))........((((.....))))-------- ( -20.32, z-score =  -0.68, R)
>droEre2.scaffold_4929 15379687 96 - 26641161
----------------GAAAAACUAUUUGGGGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUA-AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
----------------.........((((((((((((........))))))))))))(..((((((((....-(((......)))...))).)))))..)............. ( -25.40, z-score =  -2.26, R)
>droYak2.chr2L 14304262 103 + 22324452
---------CCCGCACGAAAAACUAUUUGGGGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUA-AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
---------((((((((........((((((((((((........))))))))))))........)))))..-(((......)))..........)))............... ( -29.59, z-score =  -2.43, R)
>droSec1.super_3 463613 103 + 7220098
---------CCCGCACGAAAAACUAUUUGGCGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUA-AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
---------((((((((........(((((.((((((........)))))).)))))........)))))..-(((......)))..........)))............... ( -25.89, z-score =  -1.37, R)
>droSim1.chr2L 13949342 103 + 22036055
---------CCCGCACGAAAAACUAUUUGGCGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUA-AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
---------((((((((........(((((.((((((........)))))).)))))........)))))..-(((......)))..........)))............... ( -25.89, z-score =  -1.37, R)
>consensus
_________CCCGCACGAAAAACUAUUUGGAGAGUGUUUUUUAUUGCACUCUUCAAGGCACCUGGUGUGCUA_AGCUUAUGUGCUCAAAUAUUCAGGGACAAAAUAAAAACGC
.........................((((((((((((........))))))))))))........................................................ (-10.00 = -10.27 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:39:37 2011