Locus 4125

Sequence ID dm3.chr2R
Location 10,658,335 – 10,658,427
Length 92
Max. P 0.716633
window5660 window5661

overview

Window 0

Location 10,658,335 – 10,658,427
Length 92
Sequences 9
Columns 101
Reading direction forward
Mean pairwise identity 69.49
Shannon entropy 0.61175
G+C content 0.53843
Mean single sequence MFE -24.75
Consensus MFE -11.23
Energy contribution -11.69
Covariance contribution 0.46
Combinations/Pair 1.33
Mean z-score -0.98
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.516001
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10658335 92 + 21146708
-----UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCACAAUCGAAAUCCACUGCCACGCGUGC--UCCGUGCC--GUAGAAACCGAGCACGGAUCAG
-----....(((((...))))).......((((((..........................))))))--((((((((--(.......)).))))))).... ( -25.17, z-score =  -1.26, R)
>droSim1.chr2R 9427599 92 + 19596830
-----UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCGCAAUCGAAAUCCACUGCCACGCGUGC--UCCGUGCC--GUAGAAACCGAGCACGGAUCAG
-----....(((((...))))).......((((((.....(((............)))...))))))--((((((((--(.......)).))))))).... ( -27.80, z-score =  -1.59, R)
>droSec1.super_1 8176513 92 + 14215200
-----UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCGCAAUCGAAAUCCACUGCCACGCGUGC--UCCGUGCC--GUAGAAACCGAGCACGGAUCAG
-----....(((((...))))).......((((((.....(((............)))...))))))--((((((((--(.......)).))))))).... ( -27.80, z-score =  -1.59, R)
>droYak2.chr2R 10593848 92 + 21139217
-----UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCGCAAUCGAAAUCCACUGCCACGCGUGC--UCCGUGCC--GUAGAAACCGAGCACGGAUCAG
-----....(((((...))))).......((((((.....(((............)))...))))))--((((((((--(.......)).))))))).... ( -27.80, z-score =  -1.59, R)
>droEre2.scaffold_4845 7402910 92 - 22589142
-----UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCGCAAUCGAAAUCCACUGCCACGCGUGC--UCCGUGCC--GUAGAAACCGAGCACGGAUCAG
-----....(((((...))))).......((((((.....(((............)))...))))))--((((((((--(.......)).))))))).... ( -27.80, z-score =  -1.59, R)
>dp4.chr3 4877003 89 + 19779522
-----UAAGUUAAGGAUCUGAUAU---AUUCACGCACGUCACGUCC----CUCACUGCCACGCGUGCCCUCCGUGCCCGGAAUAGAUGGGGCACGGAUCAU
-----........((...(((...---..))).((((((...((..----......))...))))))))(((((((((.(......).))))))))).... ( -27.50, z-score =  -0.85, R)
>droPer1.super_2 5069485 89 + 9036312
-----UAAGUUAAGGAUCUGAUAU---AUUCACGCACGUCACGUCC----CUCACUGCCACGCGUGCCCUCCGUGCCCGGAAUAGAUGGGGCACGGAUCAU
-----........((...(((...---..))).((((((...((..----......))...))))))))(((((((((.(......).))))))))).... ( -27.50, z-score =  -0.85, R)
>droWil1.scaffold_181141 865549 92 - 5303230
UAAGAUACUUUUGUAUUUUUGAGAUUAAUUCACGCACGUCACC-------UUCAUUGCCACGCGUGC--UCCGGAUAAUAUUGAAGAUAAAGAUGGGUGGG
.....(((((...((((((..(.((((.(((..((((((...(-------......)....))))))--...))))))).)..)))))).....))))).. ( -16.80, z-score =   0.48, R)
>droMoj3.scaffold_6496 6862860 74 - 26866924
-----UAAGUUUUGGAUCUGAUAU-UCACGCACGCCCCCU----------CACACUGCCACGCGUGU--UCAGAGACGUGUAGUAUUAUUGU---------
-----........(..(((((...-.(((((..((.....----------......))...))))).--)))))..)...............--------- ( -14.60, z-score =   0.06, R)
>consensus
_____UAAGUUCGGGAUCCGAAAUCUCACGCACGCCCUUCACAAUCGAAAUCCACUGCCACGCGUGC__UCCGUGCC__GUAGAAACCGAGCACGGAUCAG
..............................(((((..........................)))))...(((((((..............))))))).... (-11.23 = -11.69 +   0.46)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,658,335 – 10,658,427
Length 92
Sequences 9
Columns 101
Reading direction reverse
Mean pairwise identity 69.49
Shannon entropy 0.61175
G+C content 0.53843
Mean single sequence MFE -31.42
Consensus MFE -13.20
Energy contribution -14.27
Covariance contribution 1.08
Combinations/Pair 1.25
Mean z-score -1.35
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.716633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10658335 92 - 21146708
CUGAUCCGUGCUCGGUUUCUAC--GGCACGGA--GCACGCGUGGCAGUGGAUUUCGAUUGUGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA-----
....(((((((.((.......)--))))))))--((((((.(.(((((.(....).))))).)...)))))).((((..(((((...)))))))))----- ( -36.50, z-score =  -1.90, R)
>droSim1.chr2R 9427599 92 - 19596830
CUGAUCCGUGCUCGGUUUCUAC--GGCACGGA--GCACGCGUGGCAGUGGAUUUCGAUUGCGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA-----
....(((((((.((.......)--))))))))--((((((.(.(((((.(....).)))))...).)))))).((((..(((((...)))))))))----- ( -38.00, z-score =  -2.08, R)
>droSec1.super_1 8176513 92 - 14215200
CUGAUCCGUGCUCGGUUUCUAC--GGCACGGA--GCACGCGUGGCAGUGGAUUUCGAUUGCGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA-----
....(((((((.((.......)--))))))))--((((((.(.(((((.(....).)))))...).)))))).((((..(((((...)))))))))----- ( -38.00, z-score =  -2.08, R)
>droYak2.chr2R 10593848 92 - 21139217
CUGAUCCGUGCUCGGUUUCUAC--GGCACGGA--GCACGCGUGGCAGUGGAUUUCGAUUGCGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA-----
....(((((((.((.......)--))))))))--((((((.(.(((((.(....).)))))...).)))))).((((..(((((...)))))))))----- ( -38.00, z-score =  -2.08, R)
>droEre2.scaffold_4845 7402910 92 + 22589142
CUGAUCCGUGCUCGGUUUCUAC--GGCACGGA--GCACGCGUGGCAGUGGAUUUCGAUUGCGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA-----
....(((((((.((.......)--))))))))--((((((.(.(((((.(....).)))))...).)))))).((((..(((((...)))))))))----- ( -38.00, z-score =  -2.08, R)
>dp4.chr3 4877003 89 - 19779522
AUGAUCCGUGCCCCAUCUAUUCCGGGCACGGAGGGCACGCGUGGCAGUGAG----GGACGUGACGUGCGUGAAU---AUAUCAGAUCCUUAACUUA-----
.((((((((((((..........)))))))))..((.(((((.((.((...----..)))).))))).))....---...))).............----- ( -29.10, z-score =  -0.30, R)
>droPer1.super_2 5069485 89 - 9036312
AUGAUCCGUGCCCCAUCUAUUCCGGGCACGGAGGGCACGCGUGGCAGUGAG----GGACGUGACGUGCGUGAAU---AUAUCAGAUCCUUAACUUA-----
.((((((((((((..........)))))))))..((.(((((.((.((...----..)))).))))).))....---...))).............----- ( -29.10, z-score =  -0.30, R)
>droWil1.scaffold_181141 865549 92 + 5303230
CCCACCCAUCUUUAUCUUCAAUAUUAUCCGGA--GCACGCGUGGCAAUGAA-------GGUGACGUGCGUGAAUUAAUCUCAAAAAUACAAAAGUAUCUUA
..(((.(((..(((((((((.(.((((.((..--...)).)))).).))))-------))))).))).)))..............((((....)))).... ( -15.70, z-score =  -0.14, R)
>droMoj3.scaffold_6496 6862860 74 + 26866924
---------ACAAUAAUACUACACGUCUCUGA--ACACGCGUGGCAGUGUG----------AGGGGGCGUGCGUGA-AUAUCAGAUCCAAAACUUA-----
---------.......(((..(((((((((..--.(((((......)))))----------.))))))))).))).-...................----- ( -20.40, z-score =  -1.19, R)
>consensus
CUGAUCCGUGCUCGGUUUCUAC__GGCACGGA__GCACGCGUGGCAGUGGAUUUCGAUUGCGAAGGGCGUGCGUGAGAUUUCGGAUCCCGAACUUA_____
....((((((((............))))))))...(((((.(.((..............)).)...))))).............................. (-13.20 = -14.27 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:18 2011