Locus 14145

Sequence ID dm3.chrX
Location 11,443,875 – 11,443,990
Length 115
Max. P 0.931959
window19465 window19466 window19467 window19468

overview

Window 5

Location 11,443,875 – 11,443,985
Length 110
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 62.43
Shannon entropy 0.62447
G+C content 0.53928
Mean single sequence MFE -37.50
Consensus MFE -14.15
Energy contribution -14.83
Covariance contribution 0.68
Combinations/Pair 1.44
Mean z-score -1.95
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.931959
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11443875 110 + 22422827
UGCCCAAAGGGGGGCAGGAGAACCCUUCCCCCCCUGAAUGACAAGAGAAGCAGCUGGCCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUCCUCUGGCCACC---------
.(((....((((((.(((.....))).))))))......((..((((((((.((((((..(((....)))..))))))((((....))))))))))))..)).)))....--------- ( -45.00, z-score =  -2.94, R)
>droWil1.scaffold_180777 125556 90 + 4753960
---------AGUUGGAGGAGGAGGA--------AAAGGAGGCAAGAGUAGCAAAUGGUUAACUAUUUGGUAUGCCAUCUUUGUCACCAAUAUCAAUAUUAUUCUCUC------------
---------....((((((((.(..--------((((..((((....((.(((((((....))))))).))))))..))))..).))((((....)))).)))))).------------ ( -23.70, z-score =  -1.93, R)
>droAna3.scaffold_13047 190692 104 + 1816235
----UCCGGAGUGGUCGGGAGACGC----------GAGCAGU-GCAGGAGCAGCUGGGCAACUAUUUGGUAUGCCAGCGCUGUCACCAAUGCUUCUUUUCCCAGCCGCUUCUGGCCACG
----.((((((((((.((((((.(.----------(((((.(-(..(..(((((..(((((((....))).))))...)))))..))).)))))).)))))).))))).)))))..... ( -44.90, z-score =  -1.88, R)
>droEre2.scaffold_4690 15030383 101 - 18748788
-UCCCACAGGG--GCAGGAGGAGCC------CACUGAACGGUCGGAGAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUUCCCCGGCCACC---------
-.....(((((--((.......)))------).)))...((((((((((((.((((((..(((....)))..))))))((((....)))))))))).....))))))...--------- ( -40.20, z-score =  -2.24, R)
>droYak2.chrX 11052191 96 - 21770863
-UCCCAAAGGG--GCAGGAGGAGGC------CCCUGAACGA-----GAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCCUCUUUCCUCCGGCCACC---------
-.......(((--((.(((((((((------...((...((-----.((..(((((((..(((....)))..))))))))).))..))..)))....)))))).))).))--------- ( -33.70, z-score =  -0.73, R)
>consensus
__CCCAAAGGG__GCAGGAGGAGGC______C_CUGAACGGC_AGAGAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUUCUCCGGCCACC_________
.............((.((((((.......................((((((.((((((..(((....)))..))))))((((....)))))))))).)))))).))............. (-14.15 = -14.83 +   0.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,443,875 – 11,443,985
Length 110
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 62.43
Shannon entropy 0.62447
G+C content 0.53928
Mean single sequence MFE -37.06
Consensus MFE -16.00
Energy contribution -15.68
Covariance contribution -0.32
Combinations/Pair 1.42
Mean z-score -1.35
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795251
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11443875 110 - 22422827
---------GGUGGCCAGAGGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGGCCAGCUGCUUCUCUUGUCAUUCAGGGGGGGAAGGGUUCUCCUGCCCCCCUUUGGGCA
---------....(((.((.((.((((((.(((....)))(((((((..((......))..))))))))))))).)).))...(((((((((..(((....)))..)))))))))))). ( -53.70, z-score =  -3.01, R)
>droWil1.scaffold_180777 125556 90 - 4753960
------------GAGAGAAUAAUAUUGAUAUUGGUGACAAAGAUGGCAUACCAAAUAGUUAACCAUUUGCUACUCUUGCCUCCUUU--------UCCUCCUCCUCCAACU---------
------------(((.(((...........(((....))).((.((((((.(((((.(....).))))).))....))))))...)--------)))))...........--------- ( -13.50, z-score =  -0.48, R)
>droAna3.scaffold_13047 190692 104 - 1816235
CGUGGCCAGAAGCGGCUGGGAAAAGAAGCAUUGGUGACAGCGCUGGCAUACCAAAUAGUUGCCCAGCUGCUCCUGC-ACUGCUC----------GCGUCUCCCGACCACUCCGGA----
(((((((((.((((((((((......(((.(((....))).)))((....)).........)))))))))).))).-...)).)----------)))....(((.......))).---- ( -39.80, z-score =  -1.06, R)
>droEre2.scaffold_4690 15030383 101 + 18748788
---------GGUGGCCGGGGAAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUCUCCGACCGUUCAGUG------GGCUCCUCCUGC--CCCUGUGGGA-
---------((.(((.(((((..((((((.(((....)))((((((((.((......)))).))))))))))))((.((......)).------)).))).)).))--))).......- ( -38.00, z-score =  -0.79, R)
>droYak2.chrX 11052191 96 + 21770863
---------GGUGGCCGGAGGAAAGAGGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUC-----UCGUUCAGGG------GCCUCCUCCUGC--CCCUUUGGGA-
---------((.(((.((((((.((((((.(((....)))((((((((.((......)))).)))))))))))-----).(((....)------)).)))))).))--))).......- ( -40.30, z-score =  -1.40, R)
>consensus
_________GGUGGCCGGAGAAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUCUCC_ACCGUUCAG_G______GCCUCCUCCUGC__CCCUGUGGG__
.................((....((((((.(((....)))((((((...((......))...))))))))))))....))....................................... (-16.00 = -15.68 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,443,880 – 11,443,990
Length 110
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 66.08
Shannon entropy 0.54936
G+C content 0.53540
Mean single sequence MFE -36.38
Consensus MFE -14.38
Energy contribution -14.10
Covariance contribution -0.28
Combinations/Pair 1.37
Mean z-score -1.52
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.511205
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11443880 110 + 22422827
AAAGGGGGGCAGGAGAACCCUUCCCCCCCUGAAUGACAAGAGAAGCAGCUGGCCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUCC---------UCUGGCCACCGCUCU
...((((((.(((.....))).))))))......((..((((((((.((((((..(((....)))..))))))((((....))))))))))))..---------)).(((....))).. ( -41.90, z-score =  -2.01, R)
>droWil1.scaffold_180777 125561 85 + 4753960
---GAGGAGGAGGAAAAGGA-----------GGCAA---GAGUAGCAAAUGGUUAACUAUUUGGUAUGCCAUCUUUGUCACCAAUAUCAAUAUUA--------UUCUCUC---------
---(((((((.(..((((..-----------((((.---...((.(((((((....))))))).))))))..))))..).))((((....)))).--------)))))..--------- ( -23.00, z-score =  -2.31, R)
>droAna3.scaffold_13047 190697 104 + 1816235
----AGUGGUCGGGAGACGC----------GAGCAGU-GCAGGAGCAGCUGGGCAACUAUUUGGUAUGCCAGCGCUGUCACCAAUGCUUCUUUUCCCAGCCGCUUCUGGCCACGGCUCU
----.(((.((....)))))----------((((.((-((((((((.((((((........(((....)))(((.((....)).))).......)))))).)))))))..))).)))). ( -41.90, z-score =  -0.74, R)
>droEre2.scaffold_4690 15030388 101 - 18748788
---CAGGGGCAGGAGGAGCC------CACUGAACGGUCGGAGAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUUC---------CCCGGCCACCGCUCU
---(((((((.......)))------).)))...((((((((((((.((((((..(((....)))..))))))((((....))))))))))....---------.))))))........ ( -39.70, z-score =  -1.74, R)
>droYak2.chrX 11052196 96 - 21770863
---AAGGGGCAGGAGGAGGC------CCCUGAACGA-----GAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCCUCUUUCC---------UCCGGCCACCGCUCU
---..(((((.(((((((((------...((...((-----.((..(((((((..(((....)))..))))))))).))..))..)))....)))---------))).))).))..... ( -35.40, z-score =  -0.80, R)
>consensus
___GAGGGGCAGGAGGAGGC______C_CUGAACGA___GAGAAGCAGCUGGUCAACUAUUUGGUAUGCCAGCUUUGUCACCAAAGCUUCUUUUC_________UCUGGCCACCGCUCU
.......(((.(((.................................((((((..(((....)))..))))))((((....))))...................))).)))........ (-14.38 = -14.10 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,443,880 – 11,443,990
Length 110
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 66.08
Shannon entropy 0.54936
G+C content 0.53540
Mean single sequence MFE -38.18
Consensus MFE -15.64
Energy contribution -17.32
Covariance contribution 1.68
Combinations/Pair 1.24
Mean z-score -1.92
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.861771
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11443880 110 - 22422827
AGAGCGGUGGCCAGA---------GGAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGGCCAGCUGCUUCUCUUGUCAUUCAGGGGGGGAAGGGUUCUCCUGCCCCCCUUU
.(((((((((((((.---------.......(((((((....)))))))((....))......))))))).))))))............((((((((.(((.....))).)))))))). ( -50.60, z-score =  -2.64, R)
>droWil1.scaffold_180777 125561 85 - 4753960
---------GAGAGAA--------UAAUAUUGAUAUUGGUGACAAAGAUGGCAUACCAAAUAGUUAACCAUUUGCUACUC---UUGCC-----------UCCUUUUCCUCCUCCUC---
---------(((.(((--------...........(((....))).((.((((((.(((((.(....).))))).))...---.))))-----------))...))))))......--- ( -13.50, z-score =  -0.44, R)
>droAna3.scaffold_13047 190697 104 - 1816235
AGAGCCGUGGCCAGAAGCGGCUGGGAAAAGAAGCAUUGGUGACAGCGCUGGCAUACCAAAUAGUUGCCCAGCUGCUCCUGC-ACUGCUC----------GCGUCUCCCGACCACU----
.((((.(((..(((.((((((((((......(((.(((....))).)))((....)).........)))))))))).))))-)).))))----------(.(((....))))...---- ( -43.70, z-score =  -2.24, R)
>droEre2.scaffold_4690 15030388 101 + 18748788
AGAGCGGUGGCCGGG---------GAAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUCUCCGACCGUUCAGUG------GGCUCCUCCUGCCCCUG---
.(((((((...((((---------(((.((.(((((((....)))))))((((.((......)))).))..))..))))))))))))))((.(------(((.......)))))).--- ( -42.50, z-score =  -2.55, R)
>droYak2.chrX 11052196 96 + 21770863
AGAGCGGUGGCCGGA---------GGAAAGAGGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUC-----UCGUUCAGGG------GCCUCCUCCUGCCCCUU---
.....((.(((.(((---------(((.((((((.(((....)))((((((((.((......)))).)))))))))))-----).(((....)------)).)))))).)))))..--- ( -40.60, z-score =  -1.76, R)
>consensus
AGAGCGGUGGCCAGA_________GAAAAGAAGCUUUGGUGACAAAGCUGGCAUACCAAAUAGUUGACCAGCUGCUUCUC___UCGUUCAG_G______GCCUCCUCCUGCCCCUC___
.(((((((((.(((.................(((((((....)))))))((....))......))).))).)))))).......................................... (-15.64 = -17.32 +   1.68)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:34:37 2011