Locus 14106

Sequence ID dm3.chrX
Location 11,180,333 – 11,180,481
Length 148
Max. P 0.999901
window19403 window19404 window19405 window19406

overview

Window 3

Location 11,180,333 – 11,180,442
Length 109
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 84.12
Shannon entropy 0.25192
G+C content 0.32153
Mean single sequence MFE -23.99
Consensus MFE -19.08
Energy contribution -18.89
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -3.48
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.20
SVM RNA-class probability 0.997870
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11180333 109 + 22422827
AAUAUAACCUACAAAAAAAA-----AGAAUAAAAAUUAUAGCUUGGACAACAGUACGUAUGAGUAACAUCUUAGCUCACAGAUUGCUCAUACGCACCGUUGUUUC-CACUUGCGA
....................-----...............((.((((((((.((.((((((((((..((((........)))))))))))))).)).))))..))-))...)).. ( -26.40, z-score =  -3.98, R)
>droYak2.chrX 10807518 113 - 21770863
AAUAUAACUUUCAAACUAAAUUACAAUAAUAAUAAUUAGAAACUGUACAACAGUACGUAUGAGUAAUA-CUUAGCAUUCAGAUUGCUCAUACGCACCGUUGUUUU-CACUGAAGA
........(((((.............((((....))))((((....(((((.((.((((((((((((.-((........)))))))))))))).)).))))))))-)..))))). ( -24.90, z-score =  -3.51, R)
>droSec1.super_15 1865614 110 + 1954846
AAUAUAACCUAUAACUACAA-----AUAAUAAUAAUUAUAACCUGUACAACAGUACGUAUGGGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUGAGA
..............((.(((-----(((((....))))).......(((((.((.(((((((((((................))))))))))).)).))))).......))))). ( -18.99, z-score =  -1.60, R)
>droSim1.chrX_random 3137236 110 + 5698898
AAUAUAACCUAUAACUACAA-----AUAAUAAUAAUUAUAACCUGCACAACAGUGCGUAUGAGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUCAGA
....................-----.....................(((((.((((((((((((((................)))))))))))))).)))))............. ( -25.69, z-score =  -4.83, R)
>consensus
AAUAUAACCUACAAAUAAAA_____AUAAUAAUAAUUAUAACCUGUACAACAGUACGUAUGAGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUU_CACUUGAGA
..............................................(((((.((.(((((((((((................))))))))))).)).)))))............. (-19.08 = -18.89 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,180,333 – 11,180,442
Length 109
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 84.12
Shannon entropy 0.25192
G+C content 0.32153
Mean single sequence MFE -32.97
Consensus MFE -27.30
Energy contribution -28.42
Covariance contribution 1.12
Combinations/Pair 1.21
Mean z-score -3.92
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.57
SVM RNA-class probability 0.998971
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11180333 109 - 22422827
UCGCAAGUG-GAAACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAGAUGUUACUCAUACGUACUGUUGUCCAAGCUAUAAUUUUUAUUCU-----UUUUUUUUGUAGGUUAUAUU
..((...((-((..((((((((((((((((..((((........))))....)))))))))))))))))))).))((((((((.((....-----.......)).)))))))).. ( -35.00, z-score =  -4.52, R)
>droYak2.chrX 10807518 113 + 21770863
UCUUCAGUG-AAAACAACGGUGCGUAUGAGCAAUCUGAAUGCUAAG-UAUUACUCAUACGUACUGUUGUACAGUUUCUAAUUAUUAUUAUUGUAAUUUAGUUUGAAAGUUAUAUU
..(((((..-...(((((((((((((((((.(((((........))-.))).))))))))))))))))).......((((..(((((....))))))))).)))))......... ( -31.30, z-score =  -3.86, R)
>droSec1.super_15 1865614 110 - 1954846
UCUCAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACCCAUACGUACUGUUGUACAGGUUAUAAUUAUUAUUAU-----UUGUAGUUAUAGGUUAUAUU
.............(((((((((((((((((((.((((.....)))).))))...)))))))))))))))..((.((((((((((......-----..)))))))))).))..... ( -29.80, z-score =  -2.85, R)
>droSim1.chrX_random 3137236 110 - 5698898
UCUGAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACUCAUACGCACUGUUGUGCAGGUUAUAAUUAUUAUUAU-----UUGUAGUUAUAGGUUAUAUU
((((.........(((((((((((((((((..((((........))))....))))))))))))))))).))))((((((((((......-----..))))))))))........ ( -35.80, z-score =  -4.43, R)
>consensus
UCUCAAGUG_AAAACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAGAUGUUACUCAUACGUACUGUUGUACAGGUUAUAAUUAUUAUUAU_____UUGUAGUUAUAGGUUAUAUU
.............(((((((((((((((((..((((........))))....)))))))))))))))))..((.((((((((((.............)))))))))).))..... (-27.30 = -28.42 +   1.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,180,368 – 11,180,481
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 64.68
Shannon entropy 0.66024
G+C content 0.37747
Mean single sequence MFE -27.96
Consensus MFE -10.19
Energy contribution -12.81
Covariance contribution 2.61
Combinations/Pair 1.17
Mean z-score -3.24
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.63
SVM RNA-class probability 0.999071
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11180368 113 + 22422827
GCUUGGACAACAGUACGUAUGAGUAACAUCUUAGCUCACAGAUUGCUCAUACGCACCGUUGUUUC-CACUUGCGAGU------CAUUUAAACAGCUUGAAAAGCUAGGAACUUUAAAAAA
(((((((((((.((.((((((((((..((((........)))))))))))))).)).))))..))-).....(((((------..........)))))..))))................ ( -29.20, z-score =  -2.22, R)
>droAna3.scaffold_13248 2736543 102 + 4840945
----------UAACGCCCACACUGCGUA---UACGUAUUAUAUUACUCAUACGCACUGUUGCCUC-CAACCAGGACCUU----GUUUUAAAGUCCUUUUUAAAGUCGUCCUCUGGCGUAG
----------..(((((.(((.((((((---(..(((......)))..))))))).)))......-.....(((((...----.((((((((....))))))))..)))))..))))).. ( -27.90, z-score =  -4.17, R)
>droEre2.scaffold_4690 14781171 118 - 18748788
AACUGUACACCACCACGUAUGAGUUAUA-UUUAGCACGCAGAUUGCUCAUACGCACCGUUGUUUU-CACUGAAGACAUUUGCACAUUUAAGCCGUUUUAAAGGCUAGAAACUUAAAGAAA
...(((..........((((((((...(-(((.(....))))).))))))))(((....((((((-(...)))))))..))))))(((.((((........)))).)))........... ( -25.60, z-score =  -1.77, R)
>droYak2.chrX 10807558 112 - 21770863
AACUGUACAACAGUACGUAUGAGUAAUA-CUUAGCAUUCAGAUUGCUCAUACGCACCGUUGUUUU-CACUGAAGACU------CAUUUAAACAGCUUUAAAGGCUAGAAACUUUAAAAAA
.((((.....)))).((((((((((((.-((........))))))))))))))....(((((((.-...(((....)------))...)))))))(((((((........)))))))... ( -29.30, z-score =  -3.69, R)
>droSec1.super_15 1865649 105 + 1954846
ACCUGUACAACAGUACGUAUGGGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUGAGAGU------CAUUUAAAGUGUUUUAAACUUUAAAAAA---------
......(((((.((.(((((((((((................))))))))))).)).)))))(((((....))))).------..((((((((.......))))))))...--------- ( -24.79, z-score =  -2.51, R)
>droSim1.chrX_random 3137271 105 + 5698898
ACCUGCACAACAGUGCGUAUGAGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUCAGAGU------CAUUUAAAGUGCUUUAAACUUUAAAAAA---------
......(((((.((((((((((((((................)))))))))))))).)))))...............------..((((((((.......))))))))...--------- ( -30.99, z-score =  -5.06, R)
>consensus
ACCUGUACAACAGUACGUAUGAGUAACA_CUUAGCUCACAGAUUGCUCAUACGCACCGUUGUUUU_CACUUAAGACU______CAUUUAAACUGCUUUAAAAGCUAGAAACUU_AA_AAA
......(((((.((.(((((((((((................))))))))))).)).))))).......................................................... (-10.19 = -12.81 +   2.61)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,180,368 – 11,180,481
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 64.68
Shannon entropy 0.66024
G+C content 0.37747
Mean single sequence MFE -32.93
Consensus MFE -17.55
Energy contribution -18.52
Covariance contribution 0.98
Combinations/Pair 1.40
Mean z-score -3.29
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.79
SVM RNA-class probability 0.999901
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11180368 113 - 22422827
UUUUUUAAAGUUCCUAGCUUUUCAAGCUGUUUAAAUG------ACUCGCAAGUG-GAAACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAGAUGUUACUCAUACGUACUGUUGUCCAAGC
..........(((((((((.....)))))........------...(....).)-)))(((((((((((((((((..((((........))))....)))))))))))))))))...... ( -36.40, z-score =  -3.62, R)
>droAna3.scaffold_13248 2736543 102 - 4840945
CUACGCCAGAGGACGACUUUAAAAAGGACUUUAAAAC----AAGGUCCUGGUUG-GAGGCAACAGUGCGUAUGAGUAAUAUAAUACGUA---UACGCAGUGUGGGCGUUA----------
..(((((.........((((((..((((((((.....----))))))))..)))-)))...(((.((((((((.(((......))).))---)))))).))).)))))..---------- ( -39.60, z-score =  -5.52, R)
>droEre2.scaffold_4690 14781171 118 + 18748788
UUUCUUUAAGUUUCUAGCCUUUAAAACGGCUUAAAUGUGCAAAUGUCUUCAGUG-AAAACAACGGUGCGUAUGAGCAAUCUGCGUGCUAAA-UAUAACUCAUACGUGGUGGUGUACAGUU
.........((((..((((........)))).))))(((((..........((.-...))..((.((((((((((................-.....)))))))))).)).))))).... ( -25.50, z-score =  -0.16, R)
>droYak2.chrX 10807558 112 + 21770863
UUUUUUAAAGUUUCUAGCCUUUAAAGCUGUUUAAAUG------AGUCUUCAGUG-AAAACAACGGUGCGUAUGAGCAAUCUGAAUGCUAAG-UAUUACUCAUACGUACUGUUGUACAGUU
...(((((((........)))))))(((((.......------..((......)-)..(((((((((((((((((.(((((........))-.))).)))))))))))))))))))))). ( -34.50, z-score =  -4.20, R)
>droSec1.super_15 1865649 105 - 1954846
---------UUUUUUAAAGUUUAAAACACUUUAAAUG------ACUCUCAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACCCAUACGUACUGUUGUACAGGU
---------...((((((((.......))))))))..------...............(((((((((((((((((((.((((.....)))).))))...)))))))))))))))...... ( -26.90, z-score =  -2.34, R)
>droSim1.chrX_random 3137271 105 - 5698898
---------UUUUUUAAAGUUUAAAGCACUUUAAAUG------ACUCUGAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACUCAUACGCACUGUUGUGCAGGU
---------.................(((((((....------....)))))))....(((((((((((((((((..((((........))))....)))))))))))))))))...... ( -34.70, z-score =  -3.92, R)
>consensus
UUU_UU_AAGUUUCUAGCCUUUAAAGCACUUUAAAUG______ACUCUUAAGUG_AAAACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAG_UAUUACUCAUACGUACUGUUGUACAGGU
..........................................................(((((((((((((((((.(((..............))).)))))))))))))))))...... (-17.55 = -18.52 +   0.98)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:33:48 2011