Locus 12936

Sequence ID dm3.chrX
Location 3,411,364 – 3,411,479
Length 115
Max. P 0.978287
window17786 window17787 window17788

overview

Window 6

Location 3,411,364 – 3,411,463
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.13
Shannon entropy 0.35569
G+C content 0.50168
Mean single sequence MFE -33.54
Consensus MFE -17.34
Energy contribution -18.21
Covariance contribution 0.86
Combinations/Pair 1.26
Mean z-score -1.98
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.564987
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3411364 99 + 22422827
CUUGAGUUGGCCGAAGGUGACAAAAAUUCUGAACCCAGGCGUGCUGUAAGCGGUUAGUCG---GCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAA
........((((...(....)...(((((((..((((((((..((((((((.(.....).---))))))))..)))))...)))..)))))))-)).)).... ( -40.40, z-score =  -3.51, R)
>droSim1.chrX 2480861 99 + 17042790
CUUGAGUUGGCCGAAGGUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCG---GCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAA
........((((...(....)...(((((((..(((..(((..((((((((.(.....).---))))))))..))).....)))..)))))))-)).)).... ( -38.40, z-score =  -3.16, R)
>droSec1.super_4 2918155 99 - 6179234
CUUGAGUUGGCCGAAGGUGACAAAAAUUCUGAACCCAUACGUGCUGUAAGCGGUUAGUCG---GCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAA
........((((...(....)...(((((((..(((...((..((((((((.(.....).---))))))))..))......)))..)))))))-)).)).... ( -34.10, z-score =  -2.22, R)
>droYak2.chrX 16794185 99 - 21770863
CUUGAGUUGGUCGAAGGUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCG---GCUUACAGUGCGCUUCACGGGCACAGGUUU-ACACCUAAA
.((((.....))))(((((....((((.(((..(((..(((..((((((((.(.....).---))))))))..))).....)))..)))))))-.)))))... ( -35.90, z-score =  -2.57, R)
>droEre2.scaffold_4690 819637 100 + 18748788
CUUGAGCUGGUCGAAGGUGACAAAAAUUCUGAACCCAUGCGUGUUGCAAGCGGUUAGUCG---GCUUACAGUGCGCUUCACGGGCACAGGUUUUAGACCUAAA
........((((...(....).(((((.(((..(((..(((..(((.((((.(.....).---)))).)))..))).....)))..)))))))).)))).... ( -31.60, z-score =  -0.90, R)
>droAna3.scaffold_13248 3670982 82 + 4840945
CUUGAGCUCUUCGAAGGCGACAAAAAGUCUGAACACACGCGUGUUGCAAGUUCCAAGUUGCAAGUUGCCAGUUCACUGCGUG---------------------
..((((((.......((((((..........(((((....)))))((((.(....).))))..)))))))))))).......--------------------- ( -20.81, z-score =   0.48, R)
>consensus
CUUGAGUUGGCCGAAGGUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCG___GCUUACAGUGCGCUUCACGGGCAUAGGAUU_GGACCUAAA
.......((.(((..(((..............)))...(((..((((((((............))))))))..)))....))).))................. (-17.34 = -18.21 +   0.86)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,411,380 – 3,411,479
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 93.40
Shannon entropy 0.11103
G+C content 0.49785
Mean single sequence MFE -33.76
Consensus MFE -31.12
Energy contribution -31.52
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3411380 99 + 22422827
GUGACAAAAAUUCUGAACCCAGGCGUGCUGUAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAACUGCCUGAGUGACAAA
((.((...............(((((..((((((((.(.....).))))))))..)))))..((((((((((...-...))))...)))))).)).))... ( -40.60, z-score =  -3.98, R)
>droSim1.chrX 2480877 95 + 17042790
GUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAACUGUCUGAGUGA----
...((...(((((((..(((..(((..((((((((.(.....).))))))))..))).....)))..)))))))-((((.......))))..))..---- ( -34.30, z-score =  -2.67, R)
>droSec1.super_4 2918171 95 - 6179234
GUGACAAAAAUUCUGAACCCAUACGUGCUGUAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCAUAGGAUU-GGACCUAAACUGUCUGAGUGA----
...((...(((((((..(((...((..((((((((.(.....).))))))))..))......)))..)))))))-((((.......))))..))..---- ( -30.00, z-score =  -1.64, R)
>droYak2.chrX 16794201 95 - 21770863
GUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCACAGGUUU-ACACCUAAACUGCCUGAGUGA----
...................((((((..((((((((.(.....).))))))))..)))....((((((.((((..-..))))....)))))).))).---- ( -35.40, z-score =  -2.64, R)
>droEre2.scaffold_4690 819653 96 + 18748788
GUGACAAAAAUUCUGAACCCAUGCGUGUUGCAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCACAGGUUUUAGACCUAAACUGCCUGAGUGA----
...................((((((..(((.((((.(.....).)))).)))..)))....((((((.(((((...)))))....)))))).))).---- ( -28.50, z-score =  -0.38, R)
>consensus
GUGACAAAAAUUCUGAACCCAUGCGUGCUGUAAGCGGUUAGUCGGCUUACAGUGCGCUUCACGGGCAUAGGAUU_GGACCUAAACUGCCUGAGUGA____
......................(((..((((((((.(.....).))))))))..))).(((((((((((((.......))))...)))))..)))).... (-31.12 = -31.52 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,411,380 – 3,411,479
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 93.40
Shannon entropy 0.11103
G+C content 0.49785
Mean single sequence MFE -29.66
Consensus MFE -28.12
Energy contribution -27.72
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -2.22
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.978287
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3411380 99 - 22422827
UUUGUCACUCAGGCAGUUUAGGUCC-AAUCCUAUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUACAGCACGCCUGGGUUCAGAAUUUUUGUCAC
((((..((((((((.((.((((...-...)))).))..(((.......((((((((.(.....).))))))))))))))))))).))))........... ( -31.41, z-score =  -2.44, R)
>droSim1.chrX 2480877 95 - 17042790
----UCACUCAGACAGUUUAGGUCC-AAUCCUAUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUACAGCACGCAUGGGUUCAGAAUUUUUGUCAC
----.......(((((..((((...-...)))).((((((...(((..((((((((.(.....).))))))))..))))))))).........))))).. ( -30.00, z-score =  -3.15, R)
>droSec1.super_4 2918171 95 + 6179234
----UCACUCAGACAGUUUAGGUCC-AAUCCUAUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUACAGCACGUAUGGGUUCAGAAUUUUUGUCAC
----.......(((((..((((...-...)))).((((((...(((..((((((((.(.....).))))))))..))))))))).........))))).. ( -28.60, z-score =  -2.77, R)
>droYak2.chrX 16794201 95 + 21770863
----UCACUCAGGCAGUUUAGGUGU-AAACCUGUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUACAGCACGCAUGGGUUCAGAAUUUUUGUCAC
----.......(((((((((....)-))))(((.((((((...(((..((((((((.(.....).))))))))..))))))))).)))......)))).. ( -31.50, z-score =  -2.00, R)
>droEre2.scaffold_4690 819653 96 - 18748788
----UCACUCAGGCAGUUUAGGUCUAAAACCUGUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUGCAACACGCAUGGGUUCAGAAUUUUUGUCAC
----.......(((((......(((..(((((((((..(((.....)))(((((((.(.....).)))))))....))))))))).)))....))))).. ( -26.80, z-score =  -0.77, R)
>consensus
____UCACUCAGGCAGUUUAGGUCC_AAUCCUAUGCCCGUGAAGCGCACUGUAAGCCGACUAACCGCUUACAGCACGCAUGGGUUCAGAAUUUUUGUCAC
...........(((((..((((.......)))).((((((...(((..((((((((.(.....).))))))))..))))))))).........))))).. (-28.12 = -27.72 +  -0.40)

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 01:11:38 2011