Locus 8427

Sequence ID	dm3.chr3L
Location	22,662,378 – 22,662,484
Length	106
Max. P	0.995555

overview

Window 7

Location	22,662,378 – 22,662,484
Length	106
Sequences	12
Columns	108
Reading direction	forward
Mean pairwise identity	86.04
Shannon entropy	0.30491
G+C content	0.42230
Mean single sequence MFE	-27.87
Consensus MFE	-21.89
Energy contribution	-21.65
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.92
Structure conservation index	0.79
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.42
SVM RNA-class probability	0.937889
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22662378 106 + 24543557
UGUGAUGUUAACGGGUG-UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA-UUGAAUUAAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAUAGACACGCCGAUC
...........((((((-((.....(((((((((((.((....(((((.....-............))))).....)).)))))))))))......))))).)))... ( -28.93, z-score =  -2.45, R)
>droSim1.chr3L 21947670 106 + 22553184
UGUGAUGUUAACGGGUG-UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA-UUGAAUUGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGACACGCCGAUC
...........((((((-((.....(((((((((((.((....(((((.(((.-.....)))....))))).....)).)))))))))))......))))).)))... ( -30.20, z-score =  -2.77, R)
>droSec1.super_11 2578673 104 + 2888827
--UGAUGUUAACGGGUG-UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA-UUGAAUUGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGACACGCCGAUC
--.........((((((-((.....(((((((((((.((....(((((.(((.-.....)))....))))).....)).)))))))))))......))))).)))... ( -30.20, z-score =  -3.13, R)
>droYak2.chr3L 23128646 106 + 24197627
UUCGAUGUUAACGGGUG-UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA-UUGAGUUAAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGACACGCCGAUC
...........((((((-((.....(((((((((((.((....(((((.....-............))))).....)).)))))))))))......))))).)))... ( -28.93, z-score =  -2.32, R)
>droEre2.scaffold_4784 22312270 106 + 25762168
UUUGAUGUAAACGGGUG-UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA-UUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGCCACGCCGAUC
...........((((((-((.....(((((((((((.((....(((((.....-............))))).....)).))))))))))).....)).))).)))... ( -25.33, z-score =  -1.11, R)
>droAna3.scaffold_13337 22380397 106 + 23293914
AUCGGUGUUUACGGGUGUUUCUCGAAAGUAGAAUAGAAGAAUCUCACAGUGG--GUUAAAGGAACCUGUGAUAAGCCUGCUAUUCUACUUGCUAAAAACCCACCGGUC
(((((((....((((.....)))).(((((((((((.((....((((((.(.--.(.....)..))))))).....)).)))))))))))..........))))))). ( -33.10, z-score =  -2.75, R)
>droWil1.scaffold_180698 4361932 108 - 11422946
UUUGUUGUUAUCGGGUGCUUUUCGAAAGUAGAAUAGAAGAAUCUCACACCGGUUGUAAAGGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGACACACCGUUA
...........((((((((((....(((((((((((.((....(((((...(((.(....).))).))))).....)).)))))))))))...)))).))).)))... ( -29.50, z-score =  -1.87, R)
>droGri2.scaffold_15110 15103984 106 + 24565398
UGUGACGCUAGCUGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACACCAUG-UCGAAUGUUACAUGUGAUAAGCCUGCUAUUCUACUUGCCA-AUCCACACCGAUC
............((((((..((.(.(((((((((((.((....(((((...((-(........)))))))).....)).)))))))))))..).-))..))))))... ( -25.10, z-score =  -1.07, R)
>droMoj3.scaffold_6680 2679265 103 - 24764193
---GACGCUGACUGGUGCUUGUCGAAAGUAGAAUAGAAGAAUCUCACACUCGG-UCAAAUGGUACAUGUGAUAAGCCUGCUAUUCUACUUGCCA-AUCCACACCGACU
---.........(((((........(((((((((((.((....(((((.(((.-.....)))....))))).....)).)))))))))))....-.....)))))... ( -22.53, z-score =  -0.23, R)
>droVir3.scaffold_13049 8143642 103 - 25233164
---GACGCUAGCUGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACACUAGG-UUGAAUUGUACAUGUGAUAAGCCUGCUAUUCUACUUGCCA-AUCCACACCGAUC
---.........((((((..((.(.(((((((((((.((....(((((....(-(........)).))))).....)).)))))))))))..).-))..))))))... ( -25.10, z-score =  -1.16, R)
>droPer1.super_96 69850 103 - 202244
----AUGUCAACGGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCGGA-UUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAUACACACCGAUC
----.......(((((((.......(((((((((((.((....(((((..(..-..........).))))).....)).))))))))))).......)))).)))... ( -27.74, z-score =  -2.06, R)
>dp4.chrXR_group8 344175 103 + 9212921
----AUGUCAACGGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCGGA-UUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAUACACACCGAUC
----.......(((((((.......(((((((((((.((....(((((..(..-..........).))))).....)).))))))))))).......)))).)))... ( -27.74, z-score =  -2.06, R)
>consensus
U_UGAUGUUAACGGGUG_UUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGA_UUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAGACACACCGAUC
.............((((........(((((((((((.((....(((((..................))))).....)).)))))))))))..........)))).... (-21.89 = -21.65 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	22,662,378 – 22,662,484
Length	106
Sequences	12
Columns	108
Reading direction	reverse
Mean pairwise identity	86.04
Shannon entropy	0.30491
G+C content	0.42230
Mean single sequence MFE	-31.52
Consensus MFE	-19.91
Energy contribution	-20.00
Covariance contribution	0.08
Combinations/Pair	1.00
Mean z-score	-3.36
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.82
SVM RNA-class probability	0.995555
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22662378 106 - 24543557
GAUCGGCGUGUCUAUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUUAAUUCAA-UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA-CACCCGUUAACAUCACA
...(((.((((...(((.(((((((((((.(((....(((((.((.........-...)))))))...))).))))))))))))))...)-))))))........... ( -29.00, z-score =  -3.10, R)
>droSim1.chr3L 21947670 106 - 22553184
GAUCGGCGUGUCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCAAUUCAA-UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA-CACCCGUUAACAUCACA
...(((.((((..((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))..)-))))))........... ( -31.70, z-score =  -4.03, R)
>droSec1.super_11 2578673 104 - 2888827
GAUCGGCGUGUCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCAAUUCAA-UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA-CACCCGUUAACAUCA--
...(((.((((..((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))..)-)))))).........-- ( -31.70, z-score =  -4.10, R)
>droYak2.chr3L 23128646 106 - 24197627
GAUCGGCGUGUCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUUAACUCAA-UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA-CACCCGUUAACAUCGAA
...(((.((((..((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))..)-))))))........... ( -31.70, z-score =  -3.66, R)
>droEre2.scaffold_4784 22312270 106 - 25762168
GAUCGGCGUGGCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAA-UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA-CACCCGUUUACAUCAAA
...(((.(((...((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))...-))))))........... ( -29.90, z-score =  -3.04, R)
>droAna3.scaffold_13337 22380397 106 - 23293914
GACCGGUGGGUUUUUAGCAAGUAGAAUAGCAGGCUUAUCACAGGUUCCUUUAAC--CCACUGUGAGAUUCUUCUAUUCUACUUUCGAGAAACACCCGUAAACACCGAU
...(((((.((((((.(.(((((((((((.(((....((((((...........--...))))))...))).))))))))))).).)))))).........))))).. ( -34.14, z-score =  -4.05, R)
>droWil1.scaffold_180698 4361932 108 + 11422946
UAACGGUGUGUCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCCUUUACAACCGGUGUGAGAUUCUUCUAUUCUACUUUCGAAAAGCACCCGAUAACAACAAA
...(((.(((..(((.(.(((((((((((.(((....(((((((((........)))..))))))...))).))))))))))).).)))..))))))........... ( -34.40, z-score =  -4.40, R)
>droGri2.scaffold_15110 15103984 106 - 24565398
GAUCGGUGUGGAU-UGGCAAGUAGAAUAGCAGGCUUAUCACAUGUAACAUUCGA-CAUGGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGCUAGCGUCACA
....(((((...(-(((.(((((((((((.((.(((((..(((((........)-))))..)))))...)).)))))))))))))))...)))))............. ( -34.50, z-score =  -3.24, R)
>droMoj3.scaffold_6680 2679265 103 + 24764193
AGUCGGUGUGGAU-UGGCAAGUAGAAUAGCAGGCUUAUCACAUGUACCAUUUGA-CCGAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAGCACCAGUCAGCGUC---
....(((((...(-(((.(((((((((((.(((....((((((...........-....))))))...))).)))))))))))))))...)))))..........--- ( -31.46, z-score =  -2.03, R)
>droVir3.scaffold_13049 8143642 103 + 25233164
GAUCGGUGUGGAU-UGGCAAGUAGAAUAGCAGGCUUAUCACAUGUACAAUUCAA-CCUAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGCUAGCGUC---
....(((((...(-(((.(((((((((((.(((....((((((...........-....))))))...))).)))))))))))))))...)))))..........--- ( -31.16, z-score =  -2.85, R)
>droPer1.super_96 69850 103 + 202244
GAUCGGUGUGUAUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAA-UCCGCUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCCGUUGACAU----
...(((.((((..((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))...))))))).......---- ( -29.30, z-score =  -2.88, R)
>dp4.chrXR_group8 344175 103 - 9212921
GAUCGGUGUGUAUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAA-UCCGCUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCCGUUGACAU----
...(((.((((..((((.(((((((((((.(((....(((((.((.........-...)))))))...))).)))))))))))))))...))))))).......---- ( -29.30, z-score =  -2.88, R)
>consensus
GAUCGGUGUGUCUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAA_UCUGCUGUGAGAUUCUUCUAUUCUACUUUCGACAA_CACCCGUUAACAUCA_A
.......(((....(.(.(((((((((((.(((....(((((..................)))))...))).))))))))))).).)....))).............. (-19.91 = -20.00 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:45:27 2011