Locus 14164

Sequence ID dm3.chrX
Location 11,560,301 – 11,560,459
Length 158
Max. P 0.998244
window19494 window19495 window19496 window19497 window19498

overview

Window 4

Location 11,560,301 – 11,560,407
Length 106
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 72.43
Shannon entropy 0.49217
G+C content 0.48845
Mean single sequence MFE -20.25
Consensus MFE -9.34
Energy contribution -10.03
Covariance contribution 0.70
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.748542
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11560301 106 - 22422827
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUUCACAUUA---CCCCCCCCCCCCC--UGACUUCAAACAGCCCCCUCGACAAAUGUUUGUAAGCUGGCUAAUGAGCAAA--
..((((((.((((((.....)))))).).............---...........((--.(.(((((((((..............)))))).)))).))....)).)))..-- ( -18.14, z-score =  -1.53, R)
>droPer1.super_13 382510 84 + 2293547
CGGUCUGCAAAUUGCUAAUUGCAGUUCAAUAGUAGGC----------------------CGCCCCC-------CGCCUUAACCAUCGUCUGGGUGUUGCCUAAUGAGCAAAAC
((((((((.((((((.....)))))).....))))))----------------------)).....-------(((((..((....))..)))))(((((....).))))... ( -24.80, z-score =  -1.84, R)
>droSim1.chrX_random 3233091 107 - 5698898
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUCC---CCCCCCUCCCCCUU-CCCCUUCAAACAGCCCCCUCGACAAAUGUUUGUAAGCUGGCUAAUGAGCAAA--
.((((..(.((((((.....)))))).)...))))......---..............-....((((...((((..((..((((....)))).))..))))..))))....-- ( -19.30, z-score =  -2.14, R)
>droSec1.super_36 248404 111 - 449511
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUCCCCUCCCCCCUCCCCCUUCCCCCUUCAAACAGCCCCCUCGACAAAUGUUUGUAAGCUGGCUAAUGAGCAAA--
.((((..(.((((((.....)))))).)...))))..............(((......((..(((((((((..............)))))).)))..)).....)))....-- ( -19.54, z-score =  -2.27, R)
>droYak2.chrX 6645369 97 + 21770863
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUACACAUUU-------CCCCUCCACAGCCCCCUCA-------CCCUCGUCAAAUGUUUGUAAGCUGGCUAAUGAGCAAA--
..((((((.((((((.....)))))).).............-------.........((((..((.(-------(...(((...)))...)).))..))))..)).)))..-- ( -16.90, z-score =  -0.92, R)
>droEre2.scaffold_4690 15122917 90 + 18748788
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUAGCCAUUA------------------GCCCCUCAGA---GCCCCUCGUCAAAUGUAUGUAAGCUGGCUAAUGAGCAAA--
.......(.((((((.....)))))).)......(((((((------------------(((......(---((....((((....).)))...))))))))))).))...-- ( -22.80, z-score =  -1.87, R)
>consensus
AGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUUA_______CC_CCCCC___CCCCCUCAAA___CCCCCUCGACAAAUGUUUGUAAGCUGGCUAAUGAGCAAA__
.........((((((.....))))))...........................................................(((((((.((....)).))))))).... ( -9.34 = -10.03 +   0.70)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,560,335 – 11,560,443
Length 108
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 70.59
Shannon entropy 0.51974
G+C content 0.49764
Mean single sequence MFE -31.04
Consensus MFE -18.12
Energy contribution -19.02
Covariance contribution 0.89
Combinations/Pair 1.35
Mean z-score -1.83
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.93
SVM RNA-class probability 0.975455
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11560335 108 + 22422827
GGGGGCUGUUUGAAGUCAG-----GGGGGGGGGGGGUAAUGUGAAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAU--GUUUCGUUUGCUCG-
...((((......))))..-----(((.(((.((..((..(((...((.((((((((.....)))))))))).))).((((((.((....)))))))))--)..)).))).))).- ( -33.50, z-score =  -2.16, R)
>droPer1.super_13 382546 87 - 2293547
-----------------------------GGCGGGGGGCGGCCUACUAUUGAACUGCAAUUAGCAAUUUGCAGACCGUUCGUCGUGUAUUUGGUUUCAUCGAUAGAGUUUUCUCUC
-----------------------------...((((((..((...(((((((.((((((........))))))((((.............))))....))))))).))..)))))) ( -22.62, z-score =  -0.52, R)
>droSim1.chrX_random 3233125 110 + 5698898
GGGGGCUGUUUGAAGGGGAA----GGGGGAGGGGGGGGAUGUGUACUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAU--GUUUCGUUUGCUCUC
((((((....(((((.(...----................((((.....((((((((.....))))))))..)))).((((((.((....)))))))))--.)))))...)))))) ( -33.80, z-score =  -1.69, R)
>droSec1.super_36 248438 114 + 449511
GGGGGCUGUUUGAAGGGGGAAGGGGGAGGGGGGAGGGGAUGUGUACUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAU--GUUUCGUUUGCUCUC
.....((.(((.......))).)).(((((.(((.(..((((((.....((((((((.....))))))))..)))).((((((.((....)))))))).--))..).))).))))) ( -36.70, z-score =  -2.23, R)
>droYak2.chrX 6645407 96 - 21770863
-------------GAGGGG-----GCUGUGGAGGGGAAAUGUGUAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACACGUAUUUGGUUGCAU--GUUUCGUUUGCUUUC
-------------..(..(-----((.....(((.(((((((((.....((((((((.....))))))))..)))).((((((.((....)))))))).--))))).))))))..) ( -30.30, z-score =  -2.46, R)
>droEre2.scaffold_4690 15122951 93 - 18748788
----------------GGG-----GCUCUGAGGGGCUAAUGGCUAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUUGGUUGCAU--GUUUCGCUUGCUUUC
----------------..(-----((((....)))))...(((.......(((((((.....)))))))((((.((.((((((.((....)))))))).--)).))))..)))... ( -29.30, z-score =  -1.95, R)
>consensus
_____________AGGGGG_____GGGGGGGGGGGGGAAUGUGUAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAU__GUUUCGUUUGCUCUC
..............................(((((.(((((........((((((((.....)))))))).......((((((.((....)))))))).......))))).))))) (-18.12 = -19.02 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,560,335 – 11,560,443
Length 108
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 70.59
Shannon entropy 0.51974
G+C content 0.49764
Mean single sequence MFE -19.83
Consensus MFE -10.44
Energy contribution -11.13
Covariance contribution 0.69
Combinations/Pair 1.08
Mean z-score -2.86
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.30
SVM RNA-class probability 0.998244
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11560335 108 - 22422827
-CGAGCAAACGAAAC--AUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUUCACAUUACCCCCCCCCCCC-----CUGACUUCAAACAGCCCCC
-...((....(..((--.((((((((....)).)))))).))..).(.((((((.....)))))).).........................-----.............)).... ( -19.70, z-score =  -3.33, R)
>droPer1.super_13 382546 87 + 2293547
GAGAGAAAACUCUAUCGAUGAAACCAAAUACACGACGAACGGUCUGCAAAUUGCUAAUUGCAGUUCAAUAGUAGGCCGCCCCCCGCC-----------------------------
.((((....)))).(((.((..........)))))....((((((((.((((((.....)))))).....)))))))).........----------------------------- ( -19.20, z-score =  -1.84, R)
>droSim1.chrX_random 3233125 110 - 5698898
GAGAGCAAACGAAAC--AUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUCCCCCCCCUCCCCC----UUCCCCUUCAAACAGCCCCC
(((............--.((((((((....)).)))))).((((..(.((((((.....)))))).)...))))...........)))....----.................... ( -22.10, z-score =  -4.16, R)
>droSec1.super_36 248438 114 - 449511
GAGAGCAAACGAAAC--AUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUCCCCUCCCCCCUCCCCCUUCCCCCUUCAAACAGCCCCC
(((............--.((((((((....)).)))))).((((..(.((((((.....)))))).)...)))).......)))................................ ( -22.10, z-score =  -4.09, R)
>droYak2.chrX 6645407 96 + 21770863
GAAAGCAAACGAAAC--AUGCAACCAAAUACGUGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUACACAUUUCCCCUCCACAGC-----CCCCUC-------------
....((....(..((--.(((((((......).)))))).))..).(.((((((.....)))))).).......................))-----......------------- ( -17.90, z-score =  -2.32, R)
>droEre2.scaffold_4690 15122951 93 + 18748788
GAAAGCAAGCGAAAC--AUGCAACCAAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUAGCCAUUAGCCCCUCAGAGC-----CCC----------------
((..((....(..((--.(((((((......).)))))).))..).(.((((((.....)))))).).............))...)).....-----...---------------- ( -18.00, z-score =  -1.39, R)
>consensus
GAGAGCAAACGAAAC__AUGCAACCAAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAUCCCCCCCCCCCACC_____CCCCCU_____________
..................(((((((......).)))))).........((((((.....))))))................................................... (-10.44 = -11.13 +   0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,560,368 – 11,560,459
Length 91
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 76.11
Shannon entropy 0.41334
G+C content 0.42775
Mean single sequence MFE -26.14
Consensus MFE -19.12
Energy contribution -19.60
Covariance contribution 0.48
Combinations/Pair 1.30
Mean z-score -1.83
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.966289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11560368 91 + 22422827
AUGUGAAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAUGUUUCGUUUGCUCG-UUUCAAACGCAACGCA--------
..(((...((.((((((((.....)))))))))).))).((((((.((....)))))))).(((.((((((....-...)))))).)))...-------- ( -28.60, z-score =  -2.09, R)
>droPer1.super_13 382555 98 - 2293547
CGGCCUACUAUUGAACUGCAAUUAGCAAUUUGCAGACCGUUCGUCGUGUAUUUGGUUUCAUCGAUAG--AGUUUUCUCUCACUUGUCCUGCCACUGUCGG
.(((....((((((.((((((........))))))((((.............))))....))))))(--((......))).........)))........ ( -20.22, z-score =  -0.05, R)
>droSim1.chrX_random 3233159 92 + 5698898
AUGUGUACUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAUGUUUCGUUUGCUCUCUUUCAAACAGCACGCA--------
.(((((.....((((((((.....))))))))..((((.((((((.((....)))))))).))...(((((........))))).)))))))-------- ( -28.80, z-score =  -2.74, R)
>droSec1.super_36 248476 92 + 449511
AUGUGUACUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAUGUUUCGUUUGCUCUCUUUCAAACACCACGCA--------
.(((((.....((((((((.....)))))))).((.((.((((((.((....)))))))).))...(((((........))))).)))))))-------- ( -27.70, z-score =  -2.91, R)
>droYak2.chrX 6645427 97 - 21770863
AUGUGUAAUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACACGUAUUUGGUUGCAUGUUUCGUUUGCUUUCUUUCAAAUACAACACAACGCA---
.(((((......(((((((.....)))))))(((((....)).....((((((((..(((.........)))......))))))))..))).)))))--- ( -25.40, z-score =  -1.36, R)
>consensus
AUGUGUACUAUCGAACUGCAAUUAGCAGUUUGUGGCACUUGCAACUCGUAUUCGGUUGCAUGUUUCGUUUGCUCUCUUUCAAACACCACGCA________
.(((((.....((((((((.....)))))))).((.((.((((((.((....)))))))).)).))(((((........)))))...)))))........ (-19.12 = -19.60 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,560,368 – 11,560,459
Length 91
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 76.11
Shannon entropy 0.41334
G+C content 0.42775
Mean single sequence MFE -25.52
Consensus MFE -12.86
Energy contribution -14.54
Covariance contribution 1.68
Combinations/Pair 1.27
Mean z-score -1.80
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.592259
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11560368 91 - 22422827
--------UGCGUUGCGUUUGAAA-CGAGCAAACGAAACAUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUUCACAU
--------.(((((.((((((...-....)))))).))).((((((((....)).))))))...))..(.((((((.....)))))).)........... ( -25.50, z-score =  -1.83, R)
>droPer1.super_13 382555 98 + 2293547
CCGACAGUGGCAGGACAAGUGAGAGAAAACU--CUAUCGAUGAAACCAAAUACACGACGAACGGUCUGCAAAUUGCUAAUUGCAGUUCAAUAGUAGGCCG
.((...(((...((.....(((.(((....)--)).)))......)).....)))..))..((((((((.((((((.....)))))).....)))))))) ( -22.70, z-score =  -1.03, R)
>droSim1.chrX_random 3233159 92 - 5698898
--------UGCGUGCUGUUUGAAAGAGAGCAAACGAAACAUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAU
--------((.((((((((((........)))))(..((.((((((((....)).)))))).))..).(.((((((.....)))))).)..))))).)). ( -27.30, z-score =  -2.50, R)
>droSec1.super_36 248476 92 - 449511
--------UGCGUGGUGUUUGAAAGAGAGCAAACGAAACAUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAU
--------(((((((((((((........)))))...((.((((((((....)).)))))).))))))).((((((.....)))))).....)))..... ( -28.90, z-score =  -3.01, R)
>droYak2.chrX 6645427 97 + 21770863
---UGCGUUGUGUUGUAUUUGAAAGAAAGCAAACGAAACAUGCAACCAAAUACGUGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAUUACACAU
---.....(((((.(((((...............(..((.(((((((......).)))))).))..)...((((((.....)))))).))))).))))). ( -23.20, z-score =  -0.64, R)
>consensus
________UGCGUGGUGUUUGAAAGAGAGCAAACGAAACAUGCAACCGAAUACGAGUUGCAAGUGCCACAAACUGCUAAUUGCAGUUCGAUAGUACACAU
........((.(((((((.((((..............((.(((((((......).)))))).))........((((.....))))))))))))))).)). (-12.86 = -14.54 +   1.68)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:35:01 2011