Locus 3261

Sequence ID dm3.chr2R
Location 3,834,626 – 3,834,760
Length 134
Max. P 0.998772
window4487 window4488 window4489 window4490

overview

Window 7

Location 3,834,626 – 3,834,728
Length 102
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 88.40
Shannon entropy 0.19806
G+C content 0.33113
Mean single sequence MFE -31.41
Consensus MFE -26.37
Energy contribution -27.81
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -4.02
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.48
SVM RNA-class probability 0.998772
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3834626 102 + 21146708
UUAAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGCCAGGAAGUGAACACAGAGUUCAUUUCAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUAAAA
....((((((((((((((((((.....(--------(.((....)).))...)))))))))))))))))).............((((((((....))))))))....... ( -33.30, z-score =  -4.76, R)
>droSim1.chr2R 2531008 102 + 19596830
UUGAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUUAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAAUACAA
...(((((((((((((((((.((((..(--------(.((....)).)).)))))))))))))))))))))............((((((((....))))))))....... ( -29.60, z-score =  -3.81, R)
>droSec1.super_1 1471585 102 + 14215200
UUGAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUGAACACAGAGUUCAUUUUAGAUGAAUUCAUGGAAAUUAAAGCUUAUUUCUAUUACAA
...(((((((((((((((((((.(((..--------............))).)))))))))))))))))))..........((((((((........))))))))..... ( -31.34, z-score =  -4.18, R)
>droYak2.chr2L 16491552 110 + 22324452
UUGAGAAUGAGCUCUGUGUUGAAUUCGCAGAAUUCGCAGAAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAAAUGAAUUCAAGGAAAUUAACGCUUUUUUGUAUUACAA
...(((((((((((((((((.(.(((((.......)).((....))..))).).)))))))))))))))))...(((((.(((((((........))))))).))).)). ( -30.70, z-score =  -2.60, R)
>droEre2.scaffold_4929 7847440 100 - 26641161
UUGAAAAUGAGCUCUGUGUUUAAUUCGU---------AGAAGUGACAGGA-GUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAACGCUUAUUUCUAUUAUAA
...(((((((((((((((((((.(((..---------..........)))-.)))))))))))))))))))............((((((((....))))))))....... ( -32.10, z-score =  -4.77, R)
>consensus
UUGAAAAUGAGCUCUGUGUUUAAUUCGC________CAGGAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUACAA
...(((((((((((((((((((.(((......................))).)))))))))))))))))))............((((((((....))))))))....... (-26.37 = -27.81 +   1.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,834,626 – 3,834,728
Length 102
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 88.40
Shannon entropy 0.19806
G+C content 0.33113
Mean single sequence MFE -22.46
Consensus MFE -16.09
Energy contribution -16.33
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -3.12
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984510
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3834626 102 - 21146708
UUUUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUGAAAUGAACUCUGUGUUCACUUCCUGGCACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUUAA
......(((((((.(((.((((((((..((....))...)))))))).((((((((.(.((((..(.....)..--------).))).).))))))))))).))))))). ( -27.60, z-score =  -4.43, R)
>droSim1.chr2R 2531008 102 - 19596830
UUGUAUUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUAAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUCAA
.....(((....)))(..((((......))))..)....(((((((.((((((((((((((((.(......).)--------).))))).))))))))).)))))))... ( -24.00, z-score =  -3.65, R)
>droSec1.super_1 1471585 102 - 14215200
UUGUAAUAGAAAUAAGCUUUAAUUUCCAUGAAUUCAUCUAAAAUGAACUCUGUGUUCAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUCAA
........(((((........))))).............(((((((.(((((((((...(((((.........)--------).)))...))))))))).)))))))... ( -20.80, z-score =  -2.47, R)
>droYak2.chr2L 16491552 110 - 22324452
UUGUAAUACAAAAAAGCGUUAAUUUCCUUGAAUUCAUUUAAAAUGAACUCUGUGUUCACUUCCUGACACUUCUGCGAAUUCUGCGAAUUCAACACAGAGCUCAUUCUCAA
.........................................(((((.(((((((((((.....))).........((((((...)))))).)))))))).)))))..... ( -19.10, z-score =  -1.42, R)
>droEre2.scaffold_4929 7847440 100 + 26641161
UUAUAAUAGAAAUAAGCGUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCAC-UCCUGUCACUUCU---------ACGAAUUAAACACAGAGCUCAUUUUCAA
........((((..(((((((((((...((....))....))))))))((((((((...-.....((......---------..))....)))))))))))...)))).. ( -20.80, z-score =  -3.63, R)
>consensus
UUGUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCACUUCCUGACACUCCUG________GCGAAUUAAACACAGAGCUCAUUUUCAA
.......................................(((((((.(((((((((...(((......................)))...))))))))).)))))))... (-16.09 = -16.33 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,834,654 – 3,834,760
Length 106
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 78.54
Shannon entropy 0.37906
G+C content 0.31679
Mean single sequence MFE -22.12
Consensus MFE -13.06
Energy contribution -14.02
Covariance contribution 0.96
Combinations/Pair 1.13
Mean z-score -1.91
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.819068
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3834654 106 + 21146708
CAGGAGUGCCAGGAAGUGAACACAGAGUUCAUUUCAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUAAAAAUUCACCUAUGC-UUGGUAA-GCAUUAUAUGUAA--
...(..(((((((..(((((....(((((((((...)))))))))..((((((((....))))))))........))))).....)-)))))).-.)...........-- ( -27.50, z-score =  -2.69, R)
>droSim1.chr2R 2531036 110 + 19596830
CAGGAGUGUCAGGAAAUUAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAAUACAAAUUUACCUAUGCCUUGGUUUUACCUUGCCAUUAUAA
((((.((((.((((((((......(((((((((...)))))))))..((((((((....))))))))......))))).))))))))))).................... ( -23.40, z-score =  -1.55, R)
>droSec1.super_1 1471613 103 + 14215200
CAGGAGUGUCAGGAAAUGAACACAGAGUUCAUUUUAGAUGAAUUCAUGGAAAUUAAAGCUUAUUUCUAUUACAAAUUCACCUAUGCCUUGGUAA-GCAUUAUAA------
((((.((((.(((((((((((.....))))))))....((((((.((((((((........))))))))....)))))))))))))))))....-.........------ ( -23.20, z-score =  -1.95, R)
>droYak2.chr2L 16491588 102 + 22324452
CAGAAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAAAUGAAUUCAAGGAAAUUAACGCUUUUUUGUAUUACAAUUUCACUUAUAC-UUGGUAA-ACAUUAUAA------
..(((...(((.(((((((((.....)))))))))...))).)))(((((((((((..(......)..)))..))))).)))....-.......-.........------ ( -18.20, z-score =  -1.21, R)
>droEre2.scaffold_4929 7847467 84 - 26641161
UAGAAGUGACAGGA-GUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAACGCUUAUUUCUAUUAUAAUUUCACCUAUG-------------------------
...........((.-(((((....(((((((((...)))))))))..((((((((....))))))))........)))))))...------------------------- ( -18.30, z-score =  -2.13, R)
>consensus
CAGGAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUACAAAUUCACCUAUGC_UUGGUAA_ACAUUAUAA______
..(((...(((.(((((((((.....)))))))))...))).)))..((((((((....))))))))........................................... (-13.06 = -14.02 +   0.96)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,834,654 – 3,834,760
Length 106
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.54
Shannon entropy 0.37906
G+C content 0.31679
Mean single sequence MFE -17.50
Consensus MFE -11.30
Energy contribution -12.10
Covariance contribution 0.80
Combinations/Pair 1.14
Mean z-score -1.39
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.584763
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3834654 106 - 21146708
--UUACAUAUAAUGC-UUACCAA-GCAUAGGUGAAUUUUUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUGAAAUGAACUCUGUGUUCACUUCCUGGCACUCCUG
--.........((((-(.....)-))))((((((((((......(((((........)))))...))))))))))(((.(((((.....))))).)))............ ( -20.50, z-score =  -1.85, R)
>droSim1.chr2R 2531036 110 - 19596830
UUAUAAUGGCAAGGUAAAACCAAGGCAUAGGUAAAUUUGUAUUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUAAUUUCCUGACACUCCUG
.........(((((.(((...((((((((((....))))).(((....))))))))..))))))))..(((((.....)))))....((((((......))))))..... ( -16.20, z-score =   0.34, R)
>droSec1.super_1 1471613 103 - 14215200
------UUAUAAUGC-UUACCAAGGCAUAGGUGAAUUUGUAAUAGAAAUAAGCUUUAAUUUCCAUGAAUUCAUCUAAAAUGAACUCUGUGUUCAUUUCCUGACACUCCUG
------......(((-((....)))))((((((((((..(....(((((........))))).)..))))))))))((((((((.....))))))))............. ( -23.30, z-score =  -3.07, R)
>droYak2.chr2L 16491588 102 - 22324452
------UUAUAAUGU-UUACCAA-GUAUAAGUGAAAUUGUAAUACAAAAAAGCGUUAAUUUCCUUGAAUUCAUUUAAAAUGAACUCUGUGUUCACUUCCUGACACUUCUG
------......(((-(....((-((.((((.(((((((................)))))))))))..............((((.....))))))))...))))...... ( -12.59, z-score =  -0.41, R)
>droEre2.scaffold_4929 7847467 84 + 26641161
-------------------------CAUAGGUGAAAUUAUAAUAGAAAUAAGCGUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCAC-UCCUGUCACUUCUA
-------------------------...((((((..........(((...((.((((((((...((....))....)))))))).))...)))..-.....))))))... ( -14.93, z-score =  -1.94, R)
>consensus
______UUAUAAUGC_UUACCAA_GCAUAGGUGAAUUUGUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCACUUCCUGACACUCCUG
...........................((((((((((((.....(((((........)))))..))))))))))))...(((((.....)))))................ (-11.30 = -12.10 +   0.80)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:54 2011