Locus 13418

Sequence ID dm3.chrX
Location 6,445,699 – 6,445,850
Length 151
Max. P 0.851058
window18472 window18473 window18474 window18475

overview

Window 2

Location 6,445,699 – 6,445,810
Length 111
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 85.07
Shannon entropy 0.24116
G+C content 0.52506
Mean single sequence MFE -33.36
Consensus MFE -26.45
Energy contribution -27.70
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.851058
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6445699 111 + 22422827
ACUCCACUUGGACUCCACUCGCAGGCACUCAAACUUGAGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAC----ACA--UAACGAGUUGAGAGCGUAAAUGGG
...(((.(((..(((((((((.............((((((.((((....))))))))))..(((((......))))).......----...--...)))).)).)))..))).))). ( -33.60, z-score =  -1.86, R)
>droEre2.scaffold_4690 15385522 117 + 18748788
ACUCCACUUGGACUCCACUCGCAGGCACUCAAGCCUGAGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAUCUAUACAGAUACCGAGUUGAGAGCGAAAAUGGG
...(((..(((((((......(((((......))))).....)))))))((..((((....(((((......)))))....(((((....)))))..))))..))........))). ( -40.00, z-score =  -2.68, R)
>droYak2.chrX 2419797 96 + 21770863
ACUCCACUUGGACUCCACUCGCAGGCACUCAACGCUGAGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGCGCCUAUUUAC----CGAGAUACCGAG-----------------
......(((((.(((.......((((.(((.....(((((....)))))(((((((.....)).))))))).).))))......----.)))...)))))----------------- ( -24.54, z-score =  -0.99, R)
>droSec1.super_4 5832342 113 - 6179234
ACUCCACUUGGACUCCACUCGCAGGCACUCAAACUUGAGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAC----ACAGAUAUCGAGUUGAGAGCGUAAAUGGG
..(((....)))..(((.(..(..((.(((((.(((((((.((((....))))))......(((((......)))))(((((..----..))))))))))))))).)))..).))). ( -35.30, z-score =  -1.98, R)
>consensus
ACUCCACUUGGACUCCACUCGCAGGCACUCAAACCUGAGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAC____ACAGAUACCGAGUUGAGAGCGUAAAUGGG
..(((....)))(((.(((((.((((.((((....))))..((((....))))))))....(((((......)))))...................))))).)))............ (-26.45 = -27.70 +   1.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,445,699 – 6,445,810
Length 111
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 85.07
Shannon entropy 0.24116
G+C content 0.52506
Mean single sequence MFE -37.57
Consensus MFE -26.70
Energy contribution -29.95
Covariance contribution 3.25
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.819310
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6445699 111 - 22422827
CCCAUUUACGCUCUCAACUCGUUA--UGU----GUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCUCAAGUUUGAGUGCCUGCGAGUGGAGUCCAAGUGGAGU
.((((((..(((((..((((((..--((.----((.(((.((((((....)))))).)))..)))).........(..((((....))))..)..)))))))))))..))))))... ( -38.60, z-score =  -2.88, R)
>droEre2.scaffold_4690 15385522 117 - 18748788
CCCAUUUUCGCUCUCAACUCGGUAUCUGUAUAGAUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCUCAGGCUUGAGUGCCUGCGAGUGGAGUCCAAGUGGAGU
.((((((..(((((..(((((.(((((((....)))))))((((((....)))))).....((((.((....)).).)))(((((......)))))))))))))))..))))))... ( -46.00, z-score =  -3.55, R)
>droYak2.chrX 2419797 96 - 21770863
-----------------CUCGGUAUCUCG----GUAAAUAGGCGCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCUCAGCGUUGAGUGCCUGCGAGUGGAGUCCAAGUGGAGU
-----------------...((...((((----((.(((.(((.((....)).))).)))..)))......((((((((((......))))....)))))).))).))......... ( -26.60, z-score =   0.66, R)
>droSec1.super_4 5832342 113 + 6179234
CCCAUUUACGCUCUCAACUCGAUAUCUGU----GUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCUCAAGUUUGAGUGCCUGCGAGUGGAGUCCAAGUGGAGU
.((((((..(((((..(((((.(((((..----..)))))((((((....))))))...................(..((((....))))..)...))))))))))..))))))... ( -39.10, z-score =  -2.74, R)
>consensus
CCCAUUUACGCUCUCAACUCGGUAUCUGU____GUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCUCAAGUUUGAGUGCCUGCGAGUGGAGUCCAAGUGGAGU
.((((((..(((((..(((((...................((((((....))))))...................(..((((....))))..)...))))))))))..))))))... (-26.70 = -29.95 +   3.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,445,736 – 6,445,850
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 67.53
Shannon entropy 0.55436
G+C content 0.44668
Mean single sequence MFE -27.44
Consensus MFE -12.06
Energy contribution -12.82
Covariance contribution 0.76
Combinations/Pair 1.26
Mean z-score -1.38
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.599471
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6445736 114 + 22422827
AGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAC------ACAUAACGAGUUGAGAGCGUAAAUGGGUGAACUACAUUGGAAUAAAACAAGUGCUGAGACUGCAUAU
(((((.((((((((((((((....(((((......)))))..((.((------.(.....).)).)))))).....))))))))))...(((........))))))))............ ( -30.90, z-score =  -1.62, R)
>droAna3.scaffold_12929 3012084 87 + 3277472
----CGAGAUCACUUGGCUUAAUUGGCUCAAGGACGGAGCUAC----------ACGUACUUGGCA----------------GUAAUUUAUGGCAGUAGUUCGACUUCUGAUGCUUUC---
----.((((((((((((((.....))).))))....(((((((----------.......((.((----------------........)).)))))))))......)))).)))..--- ( -19.61, z-score =   0.07, R)
>droEre2.scaffold_4690 15385559 111 + 18748788
AGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAUCUAUACAGAUACCGAGUUGAGAGCGAAAAUGGGUGAUAUACAUUGAAGUAAAACAAGUGCAUAU---------
.((((..(((..((..((((....(((((......)))))....(((((....)))))..))))..)).((...((((.........))))...))..)))..))))....--------- ( -31.00, z-score =  -2.33, R)
>droYak2.chrX 2419834 99 + 21770863
AGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGCGCCUAUUUACC----GAGAUACCGAGU-----------------GAUCUACAUUGAAAUAACACAAGUGCUGAGACUGCAUAU
(((((.((.((((((((.....((((....(((.....))).....))----))....))))))-----------------)).))...(((........))))))))............ ( -23.90, z-score =  -1.50, R)
>droSec1.super_4 5832379 116 - 6179234
AGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUACA----CAGAUAUCGAGUUGAGAGCGUAAAUGGGUGAACUACAUUGAAAUAAAACAAGUGCCGUGACUGCAUAU
((((((((((((((((.((((((((((((......)))))(((((...----.)))))...)))))))........)))))))))).((((...........)))).)))).))...... ( -31.80, z-score =  -1.50, R)
>consensus
AGCACGAGUUCACUUGGCUUAAUUGGCCCAAGGACGGGCCUAUCUAC______AGAUACCGAGUUGAGAGCG_AAAUGGGUGAACUACAUUGAAAUAAAACAAGUGCUGAGACUGCAUAU
..........((((((..(((...(((((......)))))(((((........))))).....................................)))..)))))).............. (-12.06 = -12.82 +   0.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,445,736 – 6,445,850
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 67.53
Shannon entropy 0.55436
G+C content 0.44668
Mean single sequence MFE -25.57
Consensus MFE -10.40
Energy contribution -10.96
Covariance contribution 0.56
Combinations/Pair 1.20
Mean z-score -1.48
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.547458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6445736 114 - 22422827
AUAUGCAGUCUCAGCACUUGUUUUAUUCCAAUGUAGUUCACCCAUUUACGCUCUCAACUCGUUAUGU------GUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCU
............((((((((........))).(.(((((((..((((((((..............))------)))))).((((((....))))))...........))))))))))))) ( -31.84, z-score =  -3.08, R)
>droAna3.scaffold_12929 3012084 87 - 3277472
---GAAAGCAUCAGAAGUCGAACUACUGCCAUAAAUUAC----------------UGCCAAGUACGU----------GUAGCUCCGUCCUUGAGCCAAUUAAGCCAAGUGAUCUCG----
---...(((..(((.((.....)).)))..(((...(((----------------(....))))..)----------)).)))..(((((((.((.......)))))).)))....---- ( -12.70, z-score =   0.47, R)
>droEre2.scaffold_4690 15385559 111 - 18748788
---------AUAUGCACUUGUUUUACUUCAAUGUAUAUCACCCAUUUUCGCUCUCAACUCGGUAUCUGUAUAGAUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCU
---------....((((..(((((((......))).....................(((.(((((((((....)))))).((((((....))))))......))).)))))))..)))). ( -29.30, z-score =  -2.68, R)
>droYak2.chrX 2419834 99 - 21770863
AUAUGCAGUCUCAGCACUUGUGUUAUUUCAAUGUAGAUC-----------------ACUCGGUAUCUC----GGUAAAUAGGCGCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCU
............(((((..((.((((......)))).((-----------------(((.(((((...----.)).....(((.((....)).)))......))).)))))))..))))) ( -21.50, z-score =   0.40, R)
>droSec1.super_4 5832379 116 + 6179234
AUAUGCAGUCACGGCACUUGUUUUAUUUCAAUGUAGUUCACCCAUUUACGCUCUCAACUCGAUAUCUG----UGUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCU
......((.(((((((.(((........))))))(((((((..((((((((................)----))))))).((((((....))))))...........))))))))))))) ( -32.49, z-score =  -2.50, R)
>consensus
AUAUGCAGUCUCAGCACUUGUUUUAUUUCAAUGUAGUUCACCCAUUU_CGCUCUCAACUCGGUAUCU______GUAGAUAGGCCCGUCCUUGGGCCAAUUAAGCCAAGUGAACUCGUGCU
.............((((..((.(((((...................................(((............)))((((((....))))))..........)))))))..)))). (-10.40 = -10.96 +   0.56)

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 01:21:00 2011