Locus 6454

Sequence ID dm3.chr3L
Location 6,815,020 – 6,815,111
Length 91
Max. P 0.936655
window8886 window8887

overview

Window 6

Location 6,815,020 – 6,815,111
Length 91
Sequences 8
Columns 101
Reading direction forward
Mean pairwise identity 81.85
Shannon entropy 0.35082
G+C content 0.38892
Mean single sequence MFE -20.36
Consensus MFE -13.50
Energy contribution -13.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.823664
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6815020 91 + 24543557
-AAGCCGAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUU---CGUAUGUCCCGAAAUUCGUAUCGAUGUCUGGCUGAAAGUCCAUCGUGUC------
-.(((((.(((((.(((((((......(((((.....))))).---..)))))))((.....))....))))).)))))................------ ( -22.20, z-score =  -2.20, R)
>droSim1.chr3L 6296539 92 + 22553184
AAAACCGAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUU---CGUAUGUCCCGAAAUUCGAAUCGAUGUCUGGCUGCAAGUCCGACGUGUC------
.....((((..((.(((((((......(((((.....))))).---..))))))).))..)))).....(((((.(((.....))).)))))...------ ( -23.10, z-score =  -2.24, R)
>droSec1.super_2 6749166 92 + 7591821
AAAACCGAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUU---CGUAUGUCCCGAAAUUCGUAUCGAUGUCUGUCUGCAAGUCCAACGUGUC------
........((((((((((...............(((((((.((---((.......)))).))))).))(((....))).....)))))).)))).------ ( -17.40, z-score =  -1.06, R)
>droYak2.chr3L 7402425 89 + 24197627
---ACCAAACAUUUGGACAUAAAAAUUAUUUCUCAAUGAAAUU---CGUAUGUCCCGAAAUUCGUAUCGAUGUCUGGCCGAAAGUCCAUCGUGUC------
---.(((.(((((.(((((((......(((((.....))))).---..)))))))((.....))....))))).))).(....)...........------ ( -18.30, z-score =  -1.40, R)
>droEre2.scaffold_4784 21217646 92 - 25762168
AAAACCAAACAUUUGGACAUAAAAAUUAUUUCUCAAUGAAAUU---CGUAUGUCCCGAAAUUCGUAUCGAUGUCUGGCUGAAAGUCCGUCGUGUC------
....(((.(((((.(((((((......(((((.....))))).---..)))))))((.....))....))))).)))..................------ ( -17.80, z-score =  -1.30, R)
>droAna3.scaffold_13337 3199267 98 - 23293914
GACUCACAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUU---CGUAUGUCCCGAAAUUCGUAUCGAUGUCCGUCCGAGAGUCCCCGUUGCCCGUUUC
(((((.........(((((((......(((((.....))))).---..)))))))......(((...((.....))..))))))))............... ( -20.60, z-score =  -1.34, R)
>dp4.chrXR_group8 4109210 84 - 9212921
GAGGCACAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUUUUUCGUAUGUCCCGAAAUUCGUAUCGAUGCCGGACUGUCCG-----------------
..((((........(((((((..((..(((((.....)))))..))..)))))))(((........))).))))((.....)).----------------- ( -23.00, z-score =  -2.65, R)
>droPer1.super_38 588036 84 + 801819
GAGGCACAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUUUUUCGUAUGUCCCGAAAUUCGUAUCGAUGCCCGACUGUCCG-----------------
(.((((........(((((((..((..(((((.....)))))..))..)))))))(((........))).))))).........----------------- ( -20.50, z-score =  -2.28, R)
>consensus
AAAACCCAACAUUUGGACAUAAAAAUUAUUUCUGAAUGAAAUU___CGUAUGUCCCGAAAUUCGUAUCGAUGUCUGGCUGAAAGUCCAUCGUGUC______
..............(((((((......(((((.....)))))......)))))))(((........)))................................ (-13.50 = -13.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,815,020 – 6,815,111
Length 91
Sequences 8
Columns 101
Reading direction reverse
Mean pairwise identity 81.85
Shannon entropy 0.35082
G+C content 0.38892
Mean single sequence MFE -22.64
Consensus MFE -15.11
Energy contribution -14.93
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.936655
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6815020 91 - 24543557
------GACACGAUGGACUUUCAGCCAGACAUCGAUACGAAUUUCGGGACAUACG---AAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUCGGCUU-
------................((((..(((((((........)))(((((((.(---((((............))))).)))))))..))))..)))).- ( -22.20, z-score =  -2.54, R)
>droSim1.chr3L 6296539 92 - 22553184
------GACACGUCGGACUUGCAGCCAGACAUCGAUUCGAAUUUCGGGACAUACG---AAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUCGGUUUU
------.....(((((........)).)))......((((((....(((((((.(---((((............))))).)))))))....)))))).... ( -20.90, z-score =  -1.26, R)
>droSec1.super_2 6749166 92 - 7591821
------GACACGUUGGACUUGCAGACAGACAUCGAUACGAAUUUCGGGACAUACG---AAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUCGGUUUU
------(((.((.((...(((....))).)).))...(((((....(((((((.(---((((............))))).)))))))....)))))))).. ( -17.90, z-score =  -0.60, R)
>droYak2.chr3L 7402425 89 - 24197627
------GACACGAUGGACUUUCGGCCAGACAUCGAUACGAAUUUCGGGACAUACG---AAUUUCAUUGAGAAAUAAUUUUUAUGUCCAAAUGUUUGGU---
------....(((.......)))((((((((((((........)))(((((((.(---((((............))))).)))))))..)))))))))--- ( -24.60, z-score =  -2.71, R)
>droEre2.scaffold_4784 21217646 92 + 25762168
------GACACGACGGACUUUCAGCCAGACAUCGAUACGAAUUUCGGGACAUACG---AAUUUCAUUGAGAAAUAAUUUUUAUGUCCAAAUGUUUGGUUUU
------................(((((((((((((........)))(((((((.(---((((............))))).)))))))..)))))))))).. ( -23.40, z-score =  -2.76, R)
>droAna3.scaffold_13337 3199267 98 + 23293914
GAAACGGGCAACGGGGACUCUCGGACGGACAUCGAUACGAAUUUCGGGACAUACG---AAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUGUGAGUC
....(.(....).).(((((.(((.((((..(((...)))..))))(((((((.(---((((............))))).))))))).....))).))))) ( -23.40, z-score =  -0.82, R)
>dp4.chrXR_group8 4109210 84 + 9212921
-----------------CGGACAGUCCGGCAUCGAUACGAAUUUCGGGACAUACGAAAAAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUGUGCCUC
-----------------.((.....))((((.(((((((.....))(((((((.(((..(((((.....)))))..))).)))))))...))))))))).. ( -25.00, z-score =  -3.31, R)
>droPer1.super_38 588036 84 - 801819
-----------------CGGACAGUCGGGCAUCGAUACGAAUUUCGGGACAUACGAAAAAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUGUGCCUC
-----------------.........(((((.(((((((.....))(((((((.(((..(((((.....)))))..))).)))))))...)))))))))). ( -23.70, z-score =  -2.81, R)
>consensus
______GACACGAUGGACUUUCAGCCAGACAUCGAUACGAAUUUCGGGACAUACG___AAUUUCAUUCAGAAAUAAUUUUUAUGUCCAAAUGUUCGGUUUC
...........................((((((((........)))(((((((......(((((.....)))))......)))))))..)))))....... (-15.11 = -14.93 +  -0.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:08:06 2011