Locus 7839

Sequence ID dm3.chr3L
Location 17,735,474 – 17,735,603
Length 129
Max. P 0.900048
window10790 window10791 window10792

overview

Window 0

Location 17,735,474 – 17,735,571
Length 97
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 73.53
Shannon entropy 0.42969
G+C content 0.41354
Mean single sequence MFE -21.65
Consensus MFE -12.96
Energy contribution -14.65
Covariance contribution 1.69
Combinations/Pair 1.27
Mean z-score -1.80
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.900048
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17735474 97 - 24543557
----UUUACGCUGU-AAAAAUUCUUCAGUGGCAAUGGCAAUCCACCUGAAAUAUUACCCUCGCCACGGCUGAGCGAAACACAAUAAUAAAUUGUGCCUAGAC
----....((((..-...(((..((((((((..........))).)))))..)))......((....))..))))...((((((.....))))))....... ( -17.90, z-score =  -0.50, R)
>droSim1.chr3L 17069665 97 - 22553184
----UCUGUACUGUGAAAAAUUCUUCAGUGCCUCCUAGGAGGCACAC-AAAUAUUUUCCUCGCCACGGCUGAGCGAAACACAAUAAUAAAUUGUGCCUAGAC
----..(((....((((......))))(((((((....)))))))))-).....(((((((((....)).))).))))((((((.....))))))....... ( -28.20, z-score =  -3.54, R)
>droSec1.super_0 9779937 97 - 21120651
----UCUGUACUGUGAAAAAUUCUUCAGUGCCUCCUAGGAGGCACAC-AAAUAUUUUCAUCGCCACGGCUGAGCAAAACACAAUAAUAAAUUGUGCCUAGAC
----..(((...(((((((........(((((((....)))))))..-.....))))))).((....))...)))...((((((.....))))))....... ( -24.36, z-score =  -2.43, R)
>droEre2.scaffold_4784 9637135 101 + 25762168
CCAAAGAGAACCAUAGCCUUUAUGUUAUUUAGUUUAUUGUGGCACAC-AAAUACUUUCCUCGCCACGGCCGAACGAAACACAAUAAUAAAUUGUGACUAGAC
............(((((......)))))...((((.(((((((....-.............)))))))..))))....((((((.....))))))....... ( -16.13, z-score =  -0.72, R)
>consensus
____UCUGUACUGUGAAAAAUUCUUCAGUGCCUCCUAGGAGGCACAC_AAAUAUUUUCCUCGCCACGGCUGAGCGAAACACAAUAAUAAAUUGUGCCUAGAC
.............((((......))))(((((((....)))))))........((((.(((((....)).))).))))((((((.....))))))....... (-12.96 = -14.65 +   1.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,735,512 – 17,735,603
Length 91
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 59.27
Shannon entropy 0.65215
G+C content 0.36559
Mean single sequence MFE -22.08
Consensus MFE -7.06
Energy contribution -9.50
Covariance contribution 2.44
Combinations/Pair 1.33
Mean z-score -1.99
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.863242
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17735512 91 + 24543557
GGCGAGGGUA-AUAUUUCAGGUGGAUUGCCAUUGCCACUGAAGAAUUUUU-ACAGCGUAAAACACAAUAUGCUUGUACAUUACUAUAUAUAAG
(((((.((((-((...........)))))).))))).............(-((((((((........))))).))))................ ( -19.10, z-score =  -1.11, R)
>droSim1.chr3L 17069703 87 + 22553184
GGCGAGGAAA-AUAUUU-GUGUGCCUCCUAGGAGGCACUGAAGAAUUUUUCACAGUACAGAAU----UUUAUUAGUGCAUUACUAUGUAUAAA
.((...((((-(.((((-..(((((((....)))))))....)))))))))...)).......----.......((((((....))))))... ( -23.50, z-score =  -2.69, R)
>droSec1.super_0 9779975 87 + 21120651
GGCGAUGAAA-AUAUUU-GUGUGCCUCCUAGGAGGCACUGAAGAAUUUUUCACAGUACAGAAU----UUUAUUAGUGCAUUACUAUGUAUGAA
.((..(((((-(.((((-..(((((((....)))))))....))))))))))..)).......----.......((((((....))))))... ( -24.60, z-score =  -3.10, R)
>droYak2.chr3L 7874516 93 - 24197627
AAUAUUUCUGUGCCUCUCGGGAGAUUUUCGCAGUCCACUGAAGAAGUUUUACGGCCGGAAUAAACAAUUAACUUGUGGAAAAAUAUAUAGGUG
.....(((((.(((......((((((((..(((....)))..))))))))..))))))))..........(((((((........))))))). ( -21.10, z-score =  -1.04, R)
>consensus
GGCGAGGAAA_AUAUUU_GGGUGCCUCCCAGGAGCCACUGAAGAAUUUUUCACAGCACAAAAU____UUUACUAGUGCAUUACUAUAUAUAAA
..............(((((.(((((((....))))))))))))............................(((((((((....))))))))) ( -7.06 =  -9.50 +   2.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,735,512 – 17,735,603
Length 91
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 59.27
Shannon entropy 0.65215
G+C content 0.36559
Mean single sequence MFE -15.98
Consensus MFE -6.99
Energy contribution -7.67
Covariance contribution 0.69
Combinations/Pair 1.43
Mean z-score -1.22
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.819708
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17735512 91 - 24543557
CUUAUAUAUAGUAAUGUACAAGCAUAUUGUGUUUUACGCUGU-AAAAAUUCUUCAGUGGCAAUGGCAAUCCACCUGAAAUAU-UACCCUCGCC
....((((..((((..(((((.....)))))..))))..)))-)..(((..((((((((..........))).)))))..))-)......... ( -13.60, z-score =   0.27, R)
>droSim1.chr3L 17069703 87 - 22553184
UUUAUACAUAGUAAUGCACUAAUAAA----AUUCUGUACUGUGAAAAAUUCUUCAGUGCCUCCUAGGAGGCACAC-AAAUAU-UUUCCUCGCC
......(((((((.............----......)))))))............(((((((....)))))))..-......-.......... ( -19.51, z-score =  -3.11, R)
>droSec1.super_0 9779975 87 - 21120651
UUCAUACAUAGUAAUGCACUAAUAAA----AUUCUGUACUGUGAAAAAUUCUUCAGUGCCUCCUAGGAGGCACAC-AAAUAU-UUUCAUCGCC
......(((((((.............----......)))))))............(((((((....)))))))..-......-.......... ( -19.51, z-score =  -3.16, R)
>droYak2.chr3L 7874516 93 + 24197627
CACCUAUAUAUUUUUCCACAAGUUAAUUGUUUAUUCCGGCCGUAAAACUUCUUCAGUGGACUGCGAAAAUCUCCCGAGAGGCACAGAAAUAUU
.......((((((((..((((.....))))........(((.......(((..(((....))).)))..(((....))))))..)))))))). ( -11.30, z-score =   1.13, R)
>consensus
CUCAUACAUAGUAAUGCACAAAUAAA____AUUCUGCACUGUGAAAAAUUCUUCAGUGCCUCCUAGAAGGCACAC_AAAUAU_UAUCAUCGCC
.......................................................(((((((....))))))).................... ( -6.99 =  -7.67 +   0.69)

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 23:34:29 2011