Locus 10263

Sequence ID dm3.chr3R
Location 12,548,047 – 12,548,164
Length 117
Max. P 0.868494
window14111 window14112

overview

Window 1

Location 12,548,047 – 12,548,164
Length 117
Sequences 8
Columns 120
Reading direction forward
Mean pairwise identity 75.24
Shannon entropy 0.50969
G+C content 0.44561
Mean single sequence MFE -33.40
Consensus MFE -17.96
Energy contribution -18.05
Covariance contribution 0.09
Combinations/Pair 1.32
Mean z-score -1.53
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.868494
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12548047 117 + 27905053
UUUUGUCAUUCGCUCGCGAAUUUUAAAACUCUCCUGGGAGGGUUUUUU--GUUGAUUUUUGGGGGCGGUGUUUCCGCAUGUUUGCAGGCGA-UUUUUGAGGUCGUUGGUACAGUGACCGA
.....(((.((((..((((((...(((((((((....)))))))))..--..............((((.....))))..))))))..))))-....)))((((((((...)))))))).. ( -38.30, z-score =  -2.29, R)
>droSim1.chr3R 18595431 117 - 27517382
UUUUGUCAUUCGUUCGCGAAUUUUAAAACUCUCCUGGGAGGGUUUUUU--GUUGAUUUUUGGGGGCGGUGUUUCCGCAUGUUUGCAGGCGA-UUUUUGAGGUCGUUGGUACAGUGACCGA
.....(((.((((..((((((...(((((((((....)))))))))..--..............((((.....))))..))))))..))))-....)))((((((((...)))))))).. ( -36.70, z-score =  -2.07, R)
>droSec1.super_12 523927 117 - 2123299
UUUUGUCAUUCGUUCGCGAAUUUUAAAACUCUCCUGGGAGGGUUUUUU--GUUGAUUUUUGGGGGCGGUGCUUCCGCAUGUUUGCAGGCGA-UUUUUGAGGUCGUUGGUACAGUGACCGA
....(((((((((((.((((..(((((((((((....)))))))....--.))))..)))).)))))(((((...(((....))).(((((-((.....))))))))))))))))))... ( -37.40, z-score =  -2.01, R)
>droYak2.chr3R 16990665 118 - 28832112
UUUUGUCAUCCGCUUGCGAAUUUUAAAACUCUCCUGGGAGGGCUUUUU--GUUGAUUUUUGGGGGCGGCGUUUCUGCAUGUCUGCAGGCUACUUUUUCAGGUCAUUGGUACAGUGACCGA
.........((((((.((((..((((..(((((....)))))......--.))))..)))).)))))).((.((((((....))))))..)).......((((((((...)))))))).. ( -37.40, z-score =  -1.88, R)
>droEre2.scaffold_4770 8663657 120 - 17746568
UUUUGUCAUUCGUUUGCGAAUUUUAAAACUCUCCCGGGAGGGUUUUUUUUGUUGAUUUUUGGGGGCGGCGUUUCCGCAUGUUUGCAGCCGAUUUUUUGAGGUCAUUGGUACAGUGACCGA
.....(((.(((.((((((((...(((((((((....)))))))))..................((((.....))))..)))))))).))).....)))((((((((...)))))))).. ( -37.10, z-score =  -1.90, R)
>dp4.chr2 17532780 108 + 30794189
UUUUGUCAUUUGCUUGCAAAUUUUAAAACUCUCUUGGGAGGGGUCUGU------UUUUUUU-GGGUGG---UCUCGCCUGUAUGCAGACCA--UUUUAAGGUCGUUGGAACAGUGACCGA
(((((..(((((....)))))..)))))((((....)))).(((((((------......(-(((((.---...))))))...))))))).--......((((((((...)))))))).. ( -32.20, z-score =  -1.86, R)
>droPer1.super_0 11381817 109 + 11822988
UUUUGUCAUUUGCUUGCAAAUUUUAAAACUCUCUUGGGAGGGGUCUGU------UUUUUUUUGGGUGG---UCUCGGCUGUAUGCAGACCA--UUUUGAGGUCGUUGGAACAGUGACCGA
(((((..(((((....)))))..)))))((((....)))).(((((((------......(((((...---.)))))......))))))).--......((((((((...)))))))).. ( -29.50, z-score =  -0.83, R)
>droGri2.scaffold_14906 3102479 92 - 14172833
-------------------CGUUCUACACUCGUUGUUCAUCGAUGCAU-------UUUUUGUUUGUAUUGUUGCCACUUGGGGG-AGAUUU-UUAUGGAGGUCGUUGGUACAGUGACCAA
-------------------...(((...((((.....((.(((((((.-------........))))))).)).....))))..-)))...-.......((((((((...)))))))).. ( -18.60, z-score =   0.63, R)
>consensus
UUUUGUCAUUCGCUUGCGAAUUUUAAAACUCUCCUGGGAGGGUUUUUU__GUUGAUUUUUGGGGGCGGUGUUUCCGCAUGUUUGCAGGCGA_UUUUUGAGGUCGUUGGUACAGUGACCGA
.......(((((....))))).(((((((((((....)))))......................((((.....))))................))))))((((((((...)))))))).. (-17.96 = -18.05 +   0.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,548,047 – 12,548,164
Length 117
Sequences 8
Columns 120
Reading direction reverse
Mean pairwise identity 75.24
Shannon entropy 0.50969
G+C content 0.44561
Mean single sequence MFE -21.49
Consensus MFE -9.64
Energy contribution -9.95
Covariance contribution 0.31
Combinations/Pair 1.33
Mean z-score -1.48
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533394
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12548047 117 - 27905053
UCGGUCACUGUACCAACGACCUCAAAAA-UCGCCUGCAAACAUGCGGAAACACCGCCCCCAAAAAUCAAC--AAAAAACCCUCCCAGGAGAGUUUUAAAAUUCGCGAGCGAAUGACAAAA
..((((...........)))).......-((((.(((......((((.....))))..............--..(((((.(((....))).))))).......))).))))......... ( -26.50, z-score =  -3.05, R)
>droSim1.chr3R 18595431 117 + 27517382
UCGGUCACUGUACCAACGACCUCAAAAA-UCGCCUGCAAACAUGCGGAAACACCGCCCCCAAAAAUCAAC--AAAAAACCCUCCCAGGAGAGUUUUAAAAUUCGCGAACGAAUGACAAAA
..((((...........)))).......-(((..(((......((((.....))))..............--..(((((.(((....))).))))).......)))..)))......... ( -22.50, z-score =  -2.07, R)
>droSec1.super_12 523927 117 + 2123299
UCGGUCACUGUACCAACGACCUCAAAAA-UCGCCUGCAAACAUGCGGAAGCACCGCCCCCAAAAAUCAAC--AAAAAACCCUCCCAGGAGAGUUUUAAAAUUCGCGAACGAAUGACAAAA
..((((...........)))).......-(((..(((.....(((....)))..................--..(((((.(((....))).))))).......)))..)))......... ( -22.50, z-score =  -1.64, R)
>droYak2.chr3R 16990665 118 + 28832112
UCGGUCACUGUACCAAUGACCUGAAAAAGUAGCCUGCAGACAUGCAGAAACGCCGCCCCCAAAAAUCAAC--AAAAAGCCCUCCCAGGAGAGUUUUAAAAUUCGCAAGCGGAUGACAAAA
..(((((.((...)).))))).......(..(((((((....)))))....))..)..............--..(((((.(((....))).)))))...(((((....)))))....... ( -24.60, z-score =  -1.43, R)
>droEre2.scaffold_4770 8663657 120 + 17746568
UCGGUCACUGUACCAAUGACCUCAAAAAAUCGGCUGCAAACAUGCGGAAACGCCGCCCCCAAAAAUCAACAAAAAAAACCCUCCCGGGAGAGUUUUAAAAUUCGCAAACGAAUGACAAAA
..(((((.((...)).)))))........(((..(((......(((....))).....................(((((.(((....))).))))).......)))..)))......... ( -27.80, z-score =  -2.53, R)
>dp4.chr2 17532780 108 - 30794189
UCGGUCACUGUUCCAACGACCUUAAAA--UGGUCUGCAUACAGGCGAGA---CCACCC-AAAAAAA------ACAGACCCCUCCCAAGAGAGUUUUAAAAUUUGCAAGCAAAUGACAAAA
..((((...........))))((((((--((((((((......)).)))---))....-.......------........(((....))).))))))).(((((....)))))....... ( -19.90, z-score =  -1.00, R)
>droPer1.super_0 11381817 109 - 11822988
UCGGUCACUGUUCCAACGACCUCAAAA--UGGUCUGCAUACAGCCGAGA---CCACCCAAAAAAAA------ACAGACCCCUCCCAAGAGAGUUUUAAAAUUUGCAAGCAAAUGACAAAA
..((((.((((......((((......--.)))).....))))....))---))............------..((((..(((....))).))))....(((((....)))))....... ( -18.40, z-score =  -1.09, R)
>droGri2.scaffold_14906 3102479 92 + 14172833
UUGGUCACUGUACCAACGACCUCCAUAA-AAAUCU-CCCCCAAGUGGCAACAAUACAAACAAAAA-------AUGCAUCGAUGAACAACGAGUGUAGAACG-------------------
..((((...........)))).......-......-........((....)).............-------.(((((((........))).)))).....------------------- (  -9.70, z-score =   0.99, R)
>consensus
UCGGUCACUGUACCAACGACCUCAAAAA_UCGCCUGCAAACAUGCGGAAACACCGCCCCCAAAAAUCAAC__AAAAAACCCUCCCAGGAGAGUUUUAAAAUUCGCAAGCGAAUGACAAAA
..((((...........))))............((((......))))..........................((((.(.(((....))).)))))...(((((....)))))....... ( -9.64 =  -9.95 +   0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:35 2011