Locus 9745

Sequence ID dm3.chr3R
Location 8,653,119 – 8,653,316
Length 197
Max. P 0.781414
window13365 window13366 window13367

overview

Window 5

Location 8,653,119 – 8,653,211
Length 92
Sequences 7
Columns 109
Reading direction forward
Mean pairwise identity 73.34
Shannon entropy 0.47753
G+C content 0.38041
Mean single sequence MFE -20.77
Consensus MFE -11.97
Energy contribution -12.06
Covariance contribution 0.08
Combinations/Pair 1.13
Mean z-score -1.38
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781414
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8653119 92 + 27905053
-------------AAAAUACAUUUUUGGGGGUGUUUGGGUGCAUAAAAUUUAUUUACGCAUUUUUACGUUUUGCCGUGAAAUUUGCGUUGAUUGUUUGGU----GGGUC
-------------.((((((..........)))))).....(((.((((..(((.(((((.(((((((......)))))))..))))).))).)))).))----).... ( -18.00, z-score =  -0.47, R)
>droAna3.scaffold_13340 14188391 105 - 23697760
AAAUGUUUCGUUUUUUUUGUUUUUGUUGGGGUGUUGGAGCACAUAAAAUUUAUUUACGCAUUUUUACGUUUUGUCGUGAAAUUUGCGUUGAUUGUUUGGA----GGGUC
..((.((((.....................((((....))))...((((..(((.(((((.(((((((......)))))))..))))).))).)))))))----).)). ( -19.60, z-score =  -0.87, R)
>droEre2.scaffold_4770 4750405 92 - 17746568
-------------AACAGACAUUUUUUGGGGUGUUUGGGUGCAUAAAAUUUAUUUACGCAUUUUUACGUUUUGUCGUGAAAUUUGCGUUGAUUGUUUGGU----GGGUC
-------------..(((((((((....)))))))))....(((.((((..(((.(((((.(((((((......)))))))..))))).))).)))).))----).... ( -24.20, z-score =  -3.24, R)
>droSim1.chr3R 14753237 91 - 27517382
-------------AAAAGAC-UUUUUGGCGGUGUUUGGGUGCAUAAAAUUUAUUUACGCAUUUUUACGUUUUGUCGUGAAAUUUGCGUUGAUUGUUUGGU----GGGUC
-------------....(((-(..(..(((((((......)))).......(((.(((((.(((((((......)))))))..))))).))))).)..).----.)))) ( -19.80, z-score =  -1.38, R)
>dp4.chr2 19259094 88 - 30794189
---------------------UCGGGGAAAGUGUUGGGGGACAUAAAAUUUAUUUACGUAUUUUUACGUUGCGUCGUGAAAUUUGCGUUGAUUGUUUGGUCGCUGGGUC
---------------------............((.((.(((...((((..(((.(((((.(((((((......)))))))..))))).))).)))).))).)).)).. ( -19.80, z-score =  -1.04, R)
>droPer1.super_0 8983843 88 + 11822988
---------------------UCGGGGAAAGUGUUGGGGGACAUAAAAUUUAUUUACGUAUUUUUACGUUGCGUCGUGAAAUUUGCGUUGAUUGUUUGGUCGCUGGGUC
---------------------............((.((.(((...((((..(((.(((((.(((((((......)))))))..))))).))).)))).))).)).)).. ( -19.80, z-score =  -1.04, R)
>droGri2.scaffold_14906 7383386 93 - 14172833
-------------AAAGGGCAACUCUUCGGCCAAAUCGUUACGUCAAAUGUAUUUACGCAGUUUUACGUUUUGUCAUGAAAUGUGCGUUGAUUGUUAGCC--CUUGCU-
-------------.(((((((((...(((((((..((((.(((..(((((((............)))))))))).))))....)).)))))..))).)))--)))...- ( -24.20, z-score =  -1.64, R)
>consensus
_____________AAAAGAC_UUUGUGGGGGUGUUUGGGUACAUAAAAUUUAUUUACGCAUUUUUACGUUUUGUCGUGAAAUUUGCGUUGAUUGUUUGGU____GGGUC
..............................((((......)))).((((..(((.(((((.(((((((......)))))))..))))).))).))))............ (-11.97 = -12.06 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,653,119 – 8,653,211
Length 92
Sequences 7
Columns 109
Reading direction reverse
Mean pairwise identity 73.34
Shannon entropy 0.47753
G+C content 0.38041
Mean single sequence MFE -10.48
Consensus MFE -6.46
Energy contribution -6.11
Covariance contribution -0.34
Combinations/Pair 1.36
Mean z-score -1.14
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.710544
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8653119 92 - 27905053
GACCC----ACCAAACAAUCAACGCAAAUUUCACGGCAAAACGUAAAAAUGCGUAAAUAAAUUUUAUGCACCCAAACACCCCCAAAAAUGUAUUUU-------------
.....----..............(((..(((.(((......))).))).((((((((.....))))))))..................))).....------------- ( -10.60, z-score =  -1.18, R)
>droAna3.scaffold_13340 14188391 105 + 23697760
GACCC----UCCAAACAAUCAACGCAAAUUUCACGACAAAACGUAAAAAUGCGUAAAUAAAUUUUAUGUGCUCCAACACCCCAACAAAAACAAAAAAAACGAAACAUUU
.....----.........((.(((((..(((.(((......))))))..))))).............(((......))).....................))....... (  -8.60, z-score =  -1.05, R)
>droEre2.scaffold_4770 4750405 92 + 17746568
GACCC----ACCAAACAAUCAACGCAAAUUUCACGACAAAACGUAAAAAUGCGUAAAUAAAUUUUAUGCACCCAAACACCCCAAAAAAUGUCUGUU-------------
.....----....((((..((.......(((.(((......))).))).((((((((.....))))))))..................))..))))------------- ( -10.30, z-score =  -1.65, R)
>droSim1.chr3R 14753237 91 + 27517382
GACCC----ACCAAACAAUCAACGCAAAUUUCACGACAAAACGUAAAAAUGCGUAAAUAAAUUUUAUGCACCCAAACACCGCCAAAAA-GUCUUUU-------------
(((..----...................(((.(((......))).))).((((((((.....))))))))..................-)))....------------- ( -10.40, z-score =  -2.00, R)
>dp4.chr2 19259094 88 + 30794189
GACCCAGCGACCAAACAAUCAACGCAAAUUUCACGACGCAACGUAAAAAUACGUAAAUAAAUUUUAUGUCCCCCAACACUUUCCCCGA---------------------
(((...(((.............)))...............(((((....))))).............)))..................--------------------- (  -6.92, z-score =  -0.55, R)
>droPer1.super_0 8983843 88 - 11822988
GACCCAGCGACCAAACAAUCAACGCAAAUUUCACGACGCAACGUAAAAAUACGUAAAUAAAUUUUAUGUCCCCCAACACUUUCCCCGA---------------------
(((...(((.............)))...............(((((....))))).............)))..................--------------------- (  -6.92, z-score =  -0.55, R)
>droGri2.scaffold_14906 7383386 93 + 14172833
-AGCAAG--GGCUAACAAUCAACGCACAUUUCAUGACAAAACGUAAAACUGCGUAAAUACAUUUGACGUAACGAUUUGGCCGAAGAGUUGCCCUUU-------------
-...(((--(((.(((..((..((..((..((........(((((....)))))...(((.......)))..))..))..))..))))))))))).------------- ( -19.60, z-score =  -0.96, R)
>consensus
GACCC____ACCAAACAAUCAACGCAAAUUUCACGACAAAACGUAAAAAUGCGUAAAUAAAUUUUAUGUACCCAAACACCCCCAAAAA_GUCUUUU_____________
............................(((.(((......))).))).((((((((.....))))))))....................................... ( -6.46 =  -6.11 +  -0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,653,211 – 8,653,316
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 77.76
Shannon entropy 0.43646
G+C content 0.51858
Mean single sequence MFE -26.50
Consensus MFE -13.57
Energy contribution -13.21
Covariance contribution -0.36
Combinations/Pair 1.38
Mean z-score -1.56
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.513823
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8653211 105 - 27905053
GAGUGAGAAAGGUAUGUGGUCAGCCGAAAGAGAGAGCAAUACGCUGAGUGAAAGAGUGGGGCCGACGAGUAGAUUGAGUGUAAGGCCAAAGGACCAAACGACCCU
..........(((...(((((...(....)...(.((..((((((.(((......(((....).))......))).))))))..)))....)))))....))).. ( -23.90, z-score =  -1.25, R)
>droEre2.scaffold_4770 4750497 104 + 17746568
GAAUGAGAAAGGUAUGUGGUCAGACAAAAGAGACGGCAAUACACUGAGUGGAAGAGUGGAGCCGUCGAGUAGAUUGAGUGUAAGGCCAAAGUACC-AACGACCCU
..........(((((.(((((..(((.((..((((((..(((.((.......)).)))..)))))).......))...)))..)))))..)))))-......... ( -28.50, z-score =  -2.96, R)
>droYak2.chr3R 12946312 105 - 28832112
GAAUGAGAAAGGUAUGUGGUCAGCCAAACGAGAGGGCAAUAUACUGAGGGGCAGAGUGGAGCCGUCGAGUAGAUUGAGUGUAAGGCCAAAGGACCAAAAGACCCU
..........(((...(((((.......(....)(((..((((((.(..(((........)))(((.....)))).))))))..)))....)))))....))).. ( -28.40, z-score =  -1.96, R)
>droSec1.super_0 7784435 105 + 21120651
GAGUGAGAAAGGUAUGUGGUCAGUCAAAAGAGAGGGCAAUACACUGAGUGAAAGAGUGGGGCCGUCGAGUAGAUUGAGUGUAAGGCCAAAGGACCAAACGACCCU
..........(((...(((((..((......)).(((..((((((.(((.(..((.((....))))...)..))).))))))..)))....)))))....))).. ( -26.00, z-score =  -1.43, R)
>droSim1.chr3R 14753328 105 + 27517382
GAGUGAGAAAGGAAUGUGGUCAGCCGAAAGAGAGGGCAAUACACUGAGUGAAAGAGUGGGGCAGUCGAGUAGAUUGAGUGUAGGGCCAAAGGACCCAACGACCCU
.........(((..(((((((...(....)....(((..((((((.(((.(..((.((...)).))...)..))).))))))..)))....))))..)))..))) ( -26.70, z-score =  -1.30, R)
>droPer1.super_0 8983931 81 - 11822988
-------GAAGAGAGGUGG-CAGCCGA---GGAGGCUGCCUUACUGGGCAA----------UUCUGGAGGAGAUUGAGUGAGAGGCCAAGGAGC---AGGACCCU
-------....((.(((((-(((((..---...)))))))...((.(((..----------..((.((.....)).))......))).))....---...))))) ( -25.50, z-score =  -0.46, R)
>consensus
GAGUGAGAAAGGUAUGUGGUCAGCCAAAAGAGAGGGCAAUACACUGAGUGAAAGAGUGGGGCCGUCGAGUAGAUUGAGUGUAAGGCCAAAGGACCAAACGACCCU
.................((((.............(((..((((((.(((.......................))).))))))..)))............)))).. (-13.57 = -13.21 +  -0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:10:16 2011