Locus 1240

Sequence ID dm3.chr2L
Location 9,398,297 – 9,398,430
Length 133
Max. P 0.971073
window1691 window1692 window1693

overview

Window 1

Location 9,398,297 – 9,398,394
Length 97
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 75.03
Shannon entropy 0.46339
G+C content 0.48437
Mean single sequence MFE -32.88
Consensus MFE -17.88
Energy contribution -18.02
Covariance contribution 0.15
Combinations/Pair 1.48
Mean z-score -1.70
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.836538
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9398297 97 - 23011544
GCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGAAGCUUCUG-------CUCCUGCUGUUGUCGUUGCAACAGAAUGUUGCUG---GUGUGGGCAGGAUUACAAAG
(((..((((((...((.((((((((((((...(((.((....)-------)))).((....)).))))))))))))))..)).)---)))..)))............ ( -31.20, z-score =  -1.23, R)
>droSim1.chr2L 9174396 93 - 22036055
GCCAUCAUCGUUUUCCCUUUUGUUGCAGCAAUGGAAGCUCCUG----------CUGCUGCUAUCGUUGCAACAGAAUGUUGCUG---GUGU-GGCAGGAUUACAAAG
.........((..(((.((((((((((((.((((.(((.....----------..))).)))).))))))))))))(((..(..---..).-.))))))..)).... ( -33.50, z-score =  -2.48, R)
>droSec1.super_3 4852179 93 - 7220098
GCCAUCAUCGUAUUCACUUUUGUUGCAGCAAUGGAAGCUCCUG----------CUGCUGCUGUCGUUGCAACAGAAUGUUGCUG---GUGU-GGCAGGAUUACAAAG
((((.(((((((..((.((((((((((((.((((.(((.....----------..))).)))).)))))))))))))).))).)---))))-)))............ ( -34.70, z-score =  -2.39, R)
>droYak2.chr2L 12069256 102 - 22324452
GCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGCAACUGCUGCUGCU-ACUGCUGCUGAUGUCGUUGCAACAGAAUGUUGCUG---GUGU-GGCAGGAUUACAAAG
((((.((((((...((.((((((((((((...((((.(.((.((....-...)).)).).))))))))))))))))))..)).)---))))-)))............ ( -35.40, z-score =  -1.30, R)
>droEre2.scaffold_4929 10007572 93 - 26641161
GCCAUCAUCGUUUCCACUUUUGUAGCAGCAAUGGAAACUG-------------CUGCCGCUGUCGUUGCAACAGAAUGUUGCUGCUAGUGU-GGCAGGAUUACAAAG
......((((((((((...((((....)))))))))))..-------------(((((((....((.(((((.....))))).))....))-))))))))....... ( -30.90, z-score =  -1.50, R)
>droAna3.scaffold_12943 750647 100 - 5039921
GCCGUCAUCGUUUUCGCAUUUGCGGCAGUAGUAGUAGUAGUUGUAGUUGCUUUUUGUAGCUGCCACUGUUGUUGCAGGUU-UUG---GCAC-CACACGGCCACCA--
(((((.((((....)).))..)))))....(((((((((((.((((((((.....)))))))).))))))))))).(((.-..(---((..-......)))))).-- ( -31.60, z-score =  -1.32, R)
>consensus
GCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGAAGCUGCUG__________CUGCUGCUGUCGUUGCAACAGAAUGUUGCUG___GUGU_GGCAGGAUUACAAAG
(((..(((.......((((((((((((((.((((.(((.................))).)))).)))))))))))).))........)))..)))............ (-17.88 = -18.02 +   0.15)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,398,324 – 9,398,430
Length 106
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 82.48
Shannon entropy 0.32922
G+C content 0.44936
Mean single sequence MFE -30.98
Consensus MFE -18.02
Energy contribution -19.22
Covariance contribution 1.20
Combinations/Pair 1.19
Mean z-score -2.22
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.831069
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9398324 106 + 23011544
AUUCUGUUGCAACGACA------ACAGCAGGAGCAGAAGCUUCCAUUGCUGCAACAAAAGUGAAAACGAUGAUGGCUUUGGUGCCACUUCAAAUGGAAACGUUUCCACACAU
....((((((...(...------.)(((((((((....)))))...))))))))))...(((.((((((.(.((((......))))).))....(....))))).))).... ( -29.40, z-score =  -1.35, R)
>droSim1.chr2L 9174422 103 + 22036055
AUUCUGUUGCAACGAUA---------GCAGCAGCAGGAGCUUCCAUUGCUGCAACAAAAGGGAAAACGAUGAUGGCUUUGAUGCCACUUCAAAUGGAAACGUUUCCACACAU
....(((((((.((((.---------(.(((.......))).).)))).)))))))....(((((..((.(.((((......))))).))...((....)))))))...... ( -28.60, z-score =  -1.41, R)
>droSec1.super_3 4852205 103 + 7220098
AUUCUGUUGCAACGACA---------GCAGCAGCAGGAGCUUCCAUUGCUGCAACAAAAGUGAAUACGAUGAUGGCUUUGAUGCCACUUCAAAUGGAAACGUUUCCACACAG
...((((((...)))))---------)..((((((((.....))..)))))).......(((.....((.(.((((......))))).))(((((....)))))...))).. ( -30.00, z-score =  -1.75, R)
>droYak2.chr2L 12069282 112 + 22324452
AUUCUGUUGCAACGACAUCAGCAGCAGUAGCAGCAGCAGUUGCCAUUGCUGCAACAAAAGUGAAAACGAUGAUGGCUUUGAUGCCACUUCAAAUGGAAACGUUUCCACACAU
....(((((...)))))...((((((((.(((((....))))).)))))))).......(((.((((((.(.((((......))))).))....(....))))).))).... ( -37.00, z-score =  -2.58, R)
>droEre2.scaffold_4929 10007601 100 + 26641161
AUUCUGUUGCAACGAC------------AGCGGCAGCAGUUUCCAUUGCUGCUACAAAAGUGGAAACGAUGAUGGCUUUGAUGCCCCUUCAAAUGGAAACGUUUCCACACAU
...((((((...))))------------)).(((((((((....)))))))))......((((((((..(((.(((......)))...)))...(....))))))))).... ( -36.60, z-score =  -4.07, R)
>droAna3.scaffold_12943 750677 106 + 5039921
-AACAGUGGCAGCUACA-----AAAAGCAACUACAACUACUACUACUACUGCCGCAAAUGCGAAAACGAUGACGGCUUUGAUGCCACUUCAAAUGGAAACGUUCCGAUGCAU
-...((((((((((...-----...)))......................((((((....((....)).)).)))).....)))))))((.((((....))))..))..... ( -24.30, z-score =  -2.15, R)
>consensus
AUUCUGUUGCAACGACA_________GCAGCAGCAGCAGCUUCCAUUGCUGCAACAAAAGUGAAAACGAUGAUGGCUUUGAUGCCACUUCAAAUGGAAACGUUUCCACACAU
....(((((((.(((...........((....))...........))).)))))))...(((.....((...((((......))))..))(((((....)))))...))).. (-18.02 = -19.22 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,398,324 – 9,398,430
Length 106
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 82.48
Shannon entropy 0.32922
G+C content 0.44936
Mean single sequence MFE -34.02
Consensus MFE -24.78
Energy contribution -25.20
Covariance contribution 0.42
Combinations/Pair 1.36
Mean z-score -2.27
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.971073
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9398324 106 - 23011544
AUGUGUGGAAACGUUUCCAUUUGAAGUGGCACCAAAGCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGAAGCUUCUGCUCCUGCUGU------UGUCGUUGCAACAGAAU
....(((((((((.(((.....)))(((((......)))))...)))))))))((((((((((((...(((.((....))))).((...------.)).)))))))))))). ( -36.00, z-score =  -2.89, R)
>droSim1.chr2L 9174422 103 - 22036055
AUGUGUGGAAACGUUUCCAUUUGAAGUGGCAUCAAAGCCAUCAUCGUUUUCCCUUUUGUUGCAGCAAUGGAAGCUCCUGCUGCUGC---------UAUCGUUGCAACAGAAU
....((((((....))))))..((.(((((......)))))..))........((((((((((((.((((.(((.......))).)---------))).)))))))))))). ( -33.90, z-score =  -2.77, R)
>droSec1.super_3 4852205 103 - 7220098
CUGUGUGGAAACGUUUCCAUUUGAAGUGGCAUCAAAGCCAUCAUCGUAUUCACUUUUGUUGCAGCAAUGGAAGCUCCUGCUGCUGC---------UGUCGUUGCAACAGAAU
....(((((.(((.(((.....)))(((((......)))))...))).)))))((((((((((((.((((.(((.......))).)---------))).)))))))))))). ( -34.00, z-score =  -2.27, R)
>droYak2.chr2L 12069282 112 - 22324452
AUGUGUGGAAACGUUUCCAUUUGAAGUGGCAUCAAAGCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGCAACUGCUGCUGCUACUGCUGCUGAUGUCGUUGCAACAGAAU
....(((((((((.(((.....)))(((((......)))))...)))))))))((((((((((((...((((.(.((.((.......)).)).).)))))))))))))))). ( -38.80, z-score =  -2.37, R)
>droEre2.scaffold_4929 10007601 100 - 26641161
AUGUGUGGAAACGUUUCCAUUUGAAGGGGCAUCAAAGCCAUCAUCGUUUCCACUUUUGUAGCAGCAAUGGAAACUGCUGCCGCU------------GUCGUUGCAACAGAAU
....(((((((((...((.......))(((......))).....)))))))))((((((.((((((..(....))))))).((.------------......)).)))))). ( -33.80, z-score =  -2.45, R)
>droAna3.scaffold_12943 750677 106 - 5039921
AUGCAUCGGAACGUUUCCAUUUGAAGUGGCAUCAAAGCCGUCAUCGUUUUCGCAUUUGCGGCAGUAGUAGUAGUAGUUGUAGUUGCUUUU-----UGUAGCUGCCACUGUU-
.(((...(((.....)))....((.(((((......)))).).)).....(((....))))))..........((((.((((((((....-----.)))))))).))))..- ( -27.60, z-score =  -0.84, R)
>consensus
AUGUGUGGAAACGUUUCCAUUUGAAGUGGCAUCAAAGCCAUCAUCGUUUUCACUUUUGUUGCAGCAAUGGAAGCUGCUGCUGCUGC_________UGUCGUUGCAACAGAAU
....(((((((((........(((..((((......))))))).)))))))))((((((((((((.(((.........((....)).........))).)))))))))))). (-24.78 = -25.20 +   0.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:28:12 2011