Locus 6959

Sequence ID dm3.chr3L
Location 11,117,352 – 11,117,491
Length 139
Max. P 0.830075
window9580 window9581 window9582

overview

Window 0

Location 11,117,352 – 11,117,462
Length 110
Sequences 5
Columns 122
Reading direction forward
Mean pairwise identity 78.04
Shannon entropy 0.38346
G+C content 0.36083
Mean single sequence MFE -24.32
Consensus MFE -12.86
Energy contribution -13.38
Covariance contribution 0.52
Combinations/Pair 1.29
Mean z-score -2.04
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.770154
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11117352 110 + 24543557
----------UGUCAUGUAAAACGUAUUAA-AAUCGAGAGAAUAUGAAAUUCCAGUGACUCACAAGCUGGCUUCAAAUAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUGCAAAUUU-
----------.(((((......(((((...-..((....)))))))........))))).....(((((((((((.....))))((((......)))))))))))(((....)))......- ( -24.74, z-score =  -1.88, R)
>droEre2.scaffold_4784 11123979 99 + 25762168
----------------------UGUUUUCCUAAUCGAGAAAAUAAAAACUUCCAGUUACUCACUAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAUUUGCAUCCUUGAAUAUUU-
----------------------...........(((((.............(((((((.....))))))).......((((((.((((......)))).)))))).....)))))......- ( -22.30, z-score =  -3.01, R)
>droYak2.chr3L 11145911 115 + 24197627
-----CGUUUUACCAUGUAACACGUAUUCA-AAUCUAGGGAACAGAAAUCUCCAGUUAUUCACAAGCUGGCUUUAAAAAAUGAAGCCUAACUUAAGGCGCCAUUUGCAUCCUUGAAUUUUU-
-----(((.((((...)))).))).....(-(((.((((((..........((((((.......)))))).......(((((..((((......))))..)))))...)))))).))))..- ( -23.10, z-score =  -1.32, R)
>droSec1.super_0 3339754 120 + 21120651
UGUCUUACCUUACCAUGUAAAACGUAUUAA-AAUGGAAAGAAUAUGAAAUUCCAGUGACUCACGAGCUGGCUUCGAAAAAUGAAGCCUAACUUAAGGCGUCACUUGCAUCCUUA-AAUUUUG
..............((((((..........-..(((((...........)))))(((((.(..(((..(((((((.....)))))))...)))...).))))))))))).....-....... ( -24.20, z-score =  -1.74, R)
>droSim1.chr3L 10513567 115 + 22553184
-----UGUCUUACCAUGUAAAACGUAUUAA-AAUGGAGAGAAUAUGAAAUUCCAGUGACUCACAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUG-AAUUUUG
-----..((((.((((..............-.)))).))))....(((((((.((.((......(((((((((((.....))))((((......)))))))))))...)))).)-)))))). ( -27.26, z-score =  -2.24, R)
>consensus
_________UUACCAUGUAAAACGUAUUAA_AAUCGAGAGAAUAUGAAAUUCCAGUGACUCACAAGCUGGCUUCAAAAAAUGAAGCCUAACUUAAGGCGUCAGUUGCAUCCUUG_AAUUUU_
.....................................................((((((.(..(((..(((((((.....)))))))...)))...).)))))).................. (-12.86 = -13.38 +   0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,117,352 – 11,117,462
Length 110
Sequences 5
Columns 122
Reading direction reverse
Mean pairwise identity 78.04
Shannon entropy 0.38346
G+C content 0.36083
Mean single sequence MFE -26.54
Consensus MFE -15.10
Energy contribution -16.26
Covariance contribution 1.16
Combinations/Pair 1.18
Mean z-score -1.73
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.646233
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11117352 110 - 24543557
-AAAUUUGCAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUAUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCGAUU-UUAAUACGUUUUACAUGACA----------
-....(((((....))))).((((....((((((.(((((((.....)))))))))))))...))))..(((((.....))))).......-.......(((......))).---------- ( -26.10, z-score =  -1.79, R)
>droEre2.scaffold_4784 11123979 99 - 25762168
-AAAUAUUCAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUAGUGAGUAACUGGAAGUUUUUAUUUUCUCGAUUAGGAAAACA----------------------
-...(((((((((...(....)...)))).((((.(((((((.....)))))))))))...)))))..............((((((......))))))..---------------------- ( -22.60, z-score =  -1.22, R)
>droYak2.chr3L 11145911 115 - 24197627
-AAAAAUUCAAGGAUGCAAAUGGCGCCUUAAGUUAGGCUUCAUUUUUUAAAGCCAGCUUGUGAAUAACUGGAGAUUUCUGUUCCCUAGAUU-UGAAUACGUGUUACAUGGUAAAACG-----
-....(((((((...((((.((((((((......))))....((....)).))))..))))......((((.((.......)).)))).))-))))).(((.((((...)))).)))----- ( -23.00, z-score =  -0.03, R)
>droSec1.super_0 3339754 120 - 21120651
CAAAAUU-UAAGGAUGCAAGUGACGCCUUAAGUUAGGCUUCAUUUUUCGAAGCCAGCUCGUGAGUCACUGGAAUUUCAUAUUCUUUCCAUU-UUAAUACGUUUUACAUGGUAAGGUAAGACA
.......-...(((....((((((..(...((((.((((((.......))))))))))...).))))))(((((.....))))).)))...-.......(((((((........))))))). ( -31.20, z-score =  -2.84, R)
>droSim1.chr3L 10513567 115 - 22553184
CAAAAUU-CAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCCAUU-UUAAUACGUUUUACAUGGUAAGACA-----
.......-...(((......((((....((((((.(((((((.....)))))))))))))...))))..(((((.....))))).)))...-.......(((((((...))))))).----- ( -29.80, z-score =  -2.77, R)
>consensus
_AAAAUU_CAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCGAUU_UUAAUACGUUUUACAUGGUAA_________
....................((((....((((((.(((((((.....)))))))))))))...))))..(((((.....)))))...................................... (-15.10 = -16.26 +   1.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,117,371 – 11,117,491
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.15
Shannon entropy 0.34686
G+C content 0.34868
Mean single sequence MFE -28.21
Consensus MFE -16.34
Energy contribution -17.50
Covariance contribution 1.16
Combinations/Pair 1.14
Mean z-score -2.13
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830075
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11117371 120 - 24543557
CAUAGAGCGCUUAUUAAAUGAAUUUACAAAAAUUUGCAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUAUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCGAUUU
....(((.(..(((.((((..............(((((....))))).((((....((((((.(((((((.....)))))))))))))...)))).....)))).)))..).)))..... ( -28.80, z-score =  -1.53, R)
>droEre2.scaffold_4784 11123988 119 - 25762168
CAUGAGGCGUUUACUAAAAGUAUUUACUAAAAUAUUCAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUAGUGAGUAACUGGAAGUUUUUAUUUUCUCGAUU-
..(((((((((........((((((..............))))))....)))))))))((((.(((((((.....)))))))))))(((.....)))((((((....))))))......- ( -29.24, z-score =  -1.96, R)
>droYak2.chr3L 11145935 120 - 24197627
CAUAAAGCGGUUAUUAAAAGUAUUAAGUAAAAAAUUCAAGGAUGCAAAUGGCGCCUUAAGUUAGGCUUCAUUUUUUAAAGCCAGCUUGUGAAUAACUGGAGAUUUCUGUUCCCUAGAUUU
(((((.((((((.(((((((.((.((((....((((.((((.(((.....))))))).))))..)))).))))))))))))).))))))).....((((.((.......)).)))).... ( -25.80, z-score =  -0.75, R)
>droSec1.super_0 3339783 109 - 21120651
-----------CACUAAAUGAAUUUCCAACAAAAUUUAAGGAUGCAAGUGACGCCUUAAGUUAGGCUUCAUUUUUCGAAGCCAGCUCGUGAGUCACUGGAAUUUCAUAUUCUUUCCAUUU
-----------......(((((.(((((....(((((((((...(....)...))))))))).((((((.......))))))..............))))).)))))............. ( -28.20, z-score =  -3.10, R)
>droSim1.chr3L 10513591 109 - 22553184
-----------CAUUAAAUGAAUUUACAACAAAAUUCAAGGAUGCAACUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCCAUUU
-----------.......(((((((......))))))).(((......((((....((((((.(((((((.....)))))))))))))...))))..(((((.....))))).))).... ( -29.00, z-score =  -3.32, R)
>consensus
CAU___GCG_UUAUUAAAUGAAUUUACAAAAAAAUUCAAGGAUGCAAAUGACGCCUUAAGUUAGGCUUCAUUUUUUGAAGCCAGCUUGUGAGUCACUGGAAUUUCAUAUUCUCUCGAUUU
.....................((((((..........((((...(....)...))))(((((.(((((((.....))))))))))))))))))....(((((.....)))))........ (-16.34 = -17.50 +   1.16)

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 23:17:48 2011